Daily Papers

Synthetic data generation is an important application of machine learning in the field of medical imaging. While existing approaches have successfully applied fine-tuned diffusion models for synthesizing medical images, we explore potential improvements to this pipeline through feature-aligned diffusion. Our approach aligns intermediate features of the diffusion model to the output features of an expert, and our preliminary findings show an improvement of 9% in generation accuracy and ~0.12 in SSIM diversity. Our approach is also synergistic with existing methods, and easily integrated into diffusion training pipelines for improvements. We make our code available at https://github.com/lnairGT/Feature-Aligned-Diffusion.

Magnetic resonance imaging (MRI) is a crucial tool to identify brain abnormalities in a wide range of neurological disorders. In focal epilepsy MRI is used to identify structural cerebral abnormalities. For covert lesions, machine learning and artificial intelligence algorithms may improve lesion detection if abnormalities are not evident on visual inspection. The success of this approach depends on the volume and quality of training data. Herein, we release an open-source dataset of preprocessed MRI scans from 442 individuals with drug-refractory focal epilepsy who had neurosurgical resections, and detailed demographic information. The MRI scan data includes the preoperative 3D T1 and where available 3D FLAIR, as well as a manually inspected complete surface reconstruction and volumetric parcellations. Demographic information includes age, sex, age of onset of epilepsy, location of surgery, histopathology of resected specimen, occurrence and frequency of focal seizures with and without impairment of awareness, focal to bilateral tonic-clonic seizures, number of anti-seizure medications (ASMs) at time of surgery, and a total of 1764 patient years of post-surgical follow up. Crucially, we also include resection masks delineated from post-surgical imaging. To demonstrate the veracity of our data, we successfully replicated previous studies showing long-term outcomes of seizure freedom in the range of around 50%. Our imaging data replicates findings of group level atrophy in patients compared to controls. Resection locations in the cohort were predominantly in the temporal and frontal lobes. We envisage our dataset, shared openly with the community, will catalyse the development and application of computational methods in clinical neurology.

Developing and validating artificial intelligence models in medical imaging requires datasets that are large, granular, and diverse. To date, the majority of publicly available breast imaging datasets lack in one or more of these areas. Models trained on these data may therefore underperform on patient populations or pathologies that have not previously been encountered. The EMory BrEast imaging Dataset (EMBED) addresses these gaps by providing 3650,000 2D and DBT screening and diagnostic mammograms for 116,000 women divided equally between White and African American patients. The dataset also contains 40,000 annotated lesions linked to structured imaging descriptors and 61 ground truth pathologic outcomes grouped into six severity classes. Our goal is to share this dataset with research partners to aid in development and validation of breast AI models that will serve all patients fairly and help decrease bias in medical AI.

Fairness or equity in machine learning is profoundly important for societal well-being, but limited public datasets hinder its progress, especially in the area of medicine. It is undeniable that fairness in medicine is one of the most important areas for fairness learning's applications. Currently, no large-scale public medical datasets with 3D imaging data for fairness learning are available, while 3D imaging data in modern clinics are standard tests for disease diagnosis. In addition, existing medical fairness datasets are actually repurposed datasets, and therefore they typically have limited demographic identity attributes with at most three identity attributes of age, gender, and race for fairness modeling. To address this gap, we introduce our Eye Fairness dataset with 30,000 subjects (Harvard-EF) covering three major eye diseases including age-related macular degeneration, diabetic retinopathy, and glaucoma affecting 380 million patients globally. Our Harvard-EF dataset includes both 2D fundus photos and 3D optical coherence tomography scans with six demographic identity attributes including age, gender, race, ethnicity, preferred language, and marital status. We also propose a fair identity scaling (FIS) approach combining group and individual scaling together to improve model fairness. Our FIS approach is compared with various state-of-the-art fairness learning methods with superior performance in the racial, gender, and ethnicity fairness tasks with 2D and 3D imaging data, which demonstrate the utilities of our Harvard-EF dataset for fairness learning. To facilitate fairness comparisons between different models, we propose performance-scaled disparity measures, which can be used to compare model fairness accounting for overall performance levels. The dataset and code are publicly accessible via https://ophai.hms.harvard.edu/datasets/harvard-ef30k.

Large-scale medical imaging datasets have accelerated development of artificial intelligence tools for clinical decision support. However, the large size of these datasets is a bottleneck for users with limited storage and bandwidth. Many users may not even require such large datasets as AI models are often trained on lower resolution images. If users could directly download at their desired resolution, storage and bandwidth requirements would significantly decrease. However, it is impossible to anticipate every users' requirements and impractical to store the data at multiple resolutions. What if we could store images at a single resolution but send them at different ones? We propose MIST, an open-source framework to operationalize progressive resolution for streaming medical images at multiple resolutions from a single high-resolution copy. We demonstrate that MIST can dramatically reduce imaging infrastructure inefficiencies for hosting and streaming medical images by >90%, while maintaining diagnostic quality for deep learning applications.

We present FOMO60K, a large-scale, heterogeneous dataset of 60,529 brain Magnetic Resonance Imaging (MRI) scans from 13,900 sessions and 11,187 subjects, aggregated from 16 publicly available sources. The dataset includes both clinical- and research-grade images, multiple MRI sequences, and a wide range of anatomical and pathological variability, including scans with large brain anomalies. Minimal preprocessing was applied to preserve the original image characteristics while reducing barriers to entry for new users. Accompanying code for self-supervised pretraining and finetuning is provided. FOMO60K is intended to support the development and benchmarking of self-supervised learning methods in medical imaging at scale.

Hyperspectral sensors have enjoyed widespread use in the realm of remote sensing; however, they must be adapted to a format in which they can be operated onboard mobile robots. In this work, we introduce a first-of-its-kind system architecture with snapshot hyperspectral cameras and point spectrometers to efficiently generate composite datacubes from a robotic base. Our system collects and registers datacubes spanning the visible to shortwave infrared (660-1700 nm) spectrum while simultaneously capturing the ambient solar spectrum reflected off a white reference tile. We collect and disseminate a large dataset of more than 500 labeled datacubes from on-road and off-road terrain compliant with the ATLAS ontology to further the integration and demonstration of hyperspectral imaging (HSI) as beneficial in terrain class separability. Our analysis of this data demonstrates that HSI is a significant opportunity to increase understanding of scene composition from a robot-centric context. All code and data are open source online: https://river-lab.github.io/hyper_drive_data

With the rapid development of COVID-19 into a global pandemic, there is an ever more urgent need for cheap, fast and reliable tools that can assist physicians in diagnosing COVID-19. Medical imaging such as CT can take a key role in complementing conventional diagnostic tools from molecular biology, and, using deep learning techniques, several automatic systems were demonstrated promising performances using CT or X-ray data. Here, we advocate a more prominent role of point-of-care ultrasound imaging to guide COVID-19 detection. Ultrasound is non-invasive and ubiquitous in medical facilities around the globe. Our contribution is threefold. First, we gather a lung ultrasound (POCUS) dataset consisting of 1103 images (654 COVID-19, 277 bacterial pneumonia and 172 healthy controls), sampled from 64 videos. This dataset was assembled from various online sources, processed specifically for deep learning models and is intended to serve as a starting point for an open-access initiative. Second, we train a deep convolutional neural network (POCOVID-Net) on this 3-class dataset and achieve an accuracy of 89% and, by a majority vote, a video accuracy of 92% . For detecting COVID-19 in particular, the model performs with a sensitivity of 0.96, a specificity of 0.79 and F1-score of 0.92 in a 5-fold cross validation. Third, we provide an open-access web service (POCOVIDScreen) that is available at: https://pocovidscreen.org. The website deploys the predictive model, allowing to perform predictions on ultrasound lung images. In addition, it grants medical staff the option to (bulk) upload their own screenings in order to contribute to the growing public database of pathological lung ultrasound images. Dataset and code are available from: https://github.com/jannisborn/covid19_pocus_ultrasound. NOTE: This preprint is superseded by our paper in Applied Sciences: https://doi.org/10.3390/app11020672

The recent introduction of synthetic correlated diffusion (CDI^s) imaging has demonstrated significant potential in the realm of clinical decision support for prostate cancer (PCa). CDI^s is a new form of magnetic resonance imaging (MRI) designed to characterize tissue characteristics through the joint correlation of diffusion signal attenuation across different Brownian motion sensitivities. Despite the performance improvement, the CDI^s data for PCa has not been previously made publicly available. In our commitment to advance research efforts for PCa, we introduce Cancer-Net PCa-Data, an open-source benchmark dataset of volumetric CDI^s imaging data of PCa patients. Cancer-Net PCa-Data consists of CDI^s volumetric images from a patient cohort of 200 patient cases, along with full annotations (gland masks, tumor masks, and PCa diagnosis for each tumor). We also analyze the demographic and label region diversity of Cancer-Net PCa-Data for potential biases. Cancer-Net PCa-Data is the first-ever public dataset of CDI^s imaging data for PCa, and is a part of the global open-source initiative dedicated to advancement in machine learning and imaging research to aid clinicians in the global fight against cancer.

Medical researchers and clinicians often need to perform novel segmentation tasks on a set of related images. Existing methods for segmenting a new dataset are either interactive, requiring substantial human effort for each image, or require an existing set of previously labeled images. We introduce a system, MultiverSeg, that enables practitioners to rapidly segment an entire new dataset without requiring access to any existing labeled data from that task or domain. Along with the image to segment, the model takes user interactions such as clicks, bounding boxes or scribbles as input, and predicts a segmentation. As the user segments more images, those images and segmentations become additional inputs to the model, providing context. As the context set of labeled images grows, the number of interactions required to segment each new image decreases. We demonstrate that MultiverSeg enables users to interactively segment new datasets efficiently, by amortizing the number of interactions per image to achieve an accurate segmentation. Compared to using a state-of-the-art interactive segmentation method, MultiverSeg reduced the total number of clicks by 36% and scribble steps by 25% to achieve 90% Dice on sets of images from unseen tasks. We release code and model weights at https://multiverseg.csail.mit.edu

Medical imaging is essential in modern radiotherapy, supporting diagnosis, treatment planning, and monitoring. Synthetic imaging, particularly synthetic computed tomography (sCT), is gaining traction in radiotherapy. The SynthRAD2025 dataset and Grand Challenge promote advancements in sCT generation by providing a benchmarking platform for algorithms using cone-beam CT (CBCT) and magnetic resonance imaging (MRI). The dataset includes 2362 cases: 890 MRI-CT and 1472 CBCT-CT pairs from head-and-neck, thoracic, and abdominal cancer patients treated at five European university medical centers (UMC Groningen, UMC Utrecht, Radboud UMC, LMU University Hospital Munich, and University Hospital of Cologne). Data were acquired with diverse scanners and protocols. Pre-processing, including rigid and deformable image registration, ensures high-quality, modality-aligned images. Extensive quality assurance validates image consistency and usability. All imaging data is provided in MetaImage (.mha) format, ensuring compatibility with medical image processing tools. Metadata, including acquisition parameters and registration details, is available in structured CSV files. To maintain dataset integrity, SynthRAD2025 is divided into training (65%), validation (10%), and test (25%) sets. The dataset is accessible at https://doi.org/10.5281/zenodo.14918089 under the SynthRAD2025 collection. This dataset supports benchmarking and the development of synthetic imaging techniques for radiotherapy applications. Use cases include sCT generation for MRI-only and MR-guided photon/proton therapy, CBCT-based dose calculations, and adaptive radiotherapy workflows. By integrating diverse acquisition settings, SynthRAD2025 fosters robust, generalizable image synthesis algorithms, advancing personalized cancer care and adaptive radiotherapy.

Multi-modality magnetic resonance imaging data with various sequences facilitate the early diagnosis, tumor segmentation, and disease staging in the management of nasopharyngeal carcinoma (NPC). The lack of publicly available, comprehensive datasets limits advancements in diagnosis, treatment planning, and the development of machine learning algorithms for NPC. Addressing this critical need, we introduce the first comprehensive NPC MRI dataset, encompassing MR axial imaging of 277 primary NPC patients. This dataset includes T1-weighted, T2-weighted, and contrast-enhanced T1-weighted sequences, totaling 831 scans. In addition to the corresponding clinical data, manually annotated and labeled segmentations by experienced radiologists offer high-quality data resources from untreated primary NPC.

We present the data release and data reduction process for the Epoch 1 NIRCam observations for the Cosmic Evolution Early Release Science Survey (CEERS). These data consist of NIRCam imaging in six broadband filters (F115W, F150W, F200W, F277W, F356W and F444W) and one medium band filter (F410M) over four pointings, obtained in parallel with primary CEERS MIRI observations (Yang et al. in prep). We reduced the NIRCam imaging with the JWST Calibration Pipeline, with custom modifications and reduction steps designed to address additional features and challenges with the data. Here we provide a detailed description of each step in our reduction and a discussion of future expected improvements. Our reduction process includes corrections for known pre-launch issues such as 1/f noise, as well as in-flight issues including snowballs, wisps, and astrometric alignment. Many of our custom reduction processes were first developed with pre-launch simulated NIRCam imaging over the full 10 CEERS NIRCam pointings. We present a description of the creation and reduction of this simulated dataset in the Appendix. We provide mosaics of the real images in a public release, as well as our reduction scripts with detailed explanations to allow users to reproduce our final data products. These represent one of the first official public datasets released from the Directors Discretionary Early Release Science (DD-ERS) program.

Medical imaging datasets often vary due to differences in acquisition protocols, patient demographics, and imaging devices. These variations in data distribution, known as domain shift, present a significant challenge in adapting imaging analysis models for practical healthcare applications. Most current domain adaptation (DA) approaches aim either to align the distributions between the source and target domains or to learn an invariant feature space that generalizes well across all domains. However, both strategies require access to a sufficient number of examples, though not necessarily annotated, from the test domain during training. This limitation hinders the widespread deployment of models in clinical settings, where target domain data may only be accessible in real time. In this work, we introduce HyDA, a novel hypernetwork framework that leverages domain characteristics rather than suppressing them, enabling dynamic adaptation at inference time. Specifically, HyDA learns implicit domain representations and uses them to adjust model parameters on-the-fly, effectively interpolating to unseen domains. We validate HyDA on two clinically relevant applications - MRI brain age prediction and chest X-ray pathology classification - demonstrating its ability to generalize across tasks and modalities. Our code is available at TBD.

The Euclid satellite is an ESA mission that was launched in July 2023. \Euclid is working in its regular observing mode with the target of observing an area of 14,000~deg^2 with two instruments, the Visible Camera (VIS) and the Near IR Spectrometer and Photometer (NISP) down to I_{rm E} = 24.5~mag (10, sigma) in the Euclid Wide Survey. Ground-based imaging data in the ugriz bands complement the \Euclid data to enable photo-z determination and VIS PSF modeling for week lensing analysis. Euclid investigates the distance-redshift relation and the evolution of cosmic structures by measuring shapes and redshifts of galaxies and clusters of galaxies out to zsim 2. Generating the multi-wavelength catalogues from \Euclid and ground-based data is an essential part of the \Euclid data processing system. In the framework of the \Euclid Science Ground Segment (SGS), the aim of the MER Processing Function (PF) pipeline is to detect objects in the \Euclid imaging data, measure their properties, and MERge them into a single multi-wavelength catalogue. The MER PF pipeline performs source detection on both visible (VIS) and near-infrared (NIR) images and offers four different photometric measurements: Kron total flux, aperture photometry on PSF-matched images, template fitting photometry, and S\'ersic fitting photometry. Furthermore, the MER PF pipeline measures a set of ancillary quantities, spanning from morphology to quality flags, to better characterise all detected sources. In this paper, we show how the MER PF pipeline is designed, detailing its main steps, and we show that the pipeline products meet the tight requirements that Euclid aims to achieve on photometric accuracy. We also present the other measurements (e.g. morphology) that are included in the OU-MER output catalogues and we list all output products coming out of the MER PF pipeline.

Multi-modal three-dimensional (3D) medical imaging data, derived from ultrasound, magnetic resonance imaging (MRI), and potentially computed tomography (CT), provide a widely adopted approach for non-invasive anatomical visualization. Accurate modeling, registration, and visualization in this setting depend on surface reconstruction and frame-to-frame interpolation. Traditional methods often face limitations due to image noise and incomplete information between frames. To address these challenges, we present MedGS, a semi-supervised neural implicit surface reconstruction framework that employs a Gaussian Splatting (GS)-based interpolation mechanism. In this framework, medical imaging data are represented as consecutive two-dimensional (2D) frames embedded in 3D space and modeled using Gaussian-based distributions. This representation enables robust frame interpolation and high-fidelity surface reconstruction across imaging modalities. As a result, MedGS offers more efficient training than traditional neural implicit methods. Its explicit GS-based representation enhances noise robustness, allows flexible editing, and supports precise modeling of complex anatomical structures with fewer artifacts. These features make MedGS highly suitable for scalable and practical applications in medical imaging.

Breast cancer remains a leading cause of cancer-related mortality worldwide, making early detection and accurate treatment response monitoring critical priorities. We present BreastDCEDL, a curated, deep learning-ready dataset comprising pre-treatment 3D Dynamic Contrast-Enhanced MRI (DCE-MRI) scans from 2,070 breast cancer patients drawn from the I-SPY1, I-SPY2, and Duke cohorts, all sourced from The Cancer Imaging Archive. The raw DICOM imaging data were rigorously converted into standardized 3D NIfTI volumes with preserved signal integrity, accompanied by unified tumor annotations and harmonized clinical metadata including pathologic complete response (pCR), hormone receptor (HR), and HER2 status. Although DCE-MRI provides essential diagnostic information and deep learning offers tremendous potential for analyzing such complex data, progress has been limited by lack of accessible, public, multicenter datasets. BreastDCEDL addresses this gap by enabling development of advanced models, including state-of-the-art transformer architectures that require substantial training data. To demonstrate its capacity for robust modeling, we developed the first transformer-based model for breast DCE-MRI, leveraging Vision Transformer (ViT) architecture trained on RGB-fused images from three contrast phases (pre-contrast, early post-contrast, and late post-contrast). Our ViT model achieved state-of-the-art pCR prediction performance in HR+/HER2- patients (AUC 0.94, accuracy 0.93). BreastDCEDL includes predefined benchmark splits, offering a framework for reproducible research and enabling clinically meaningful modeling in breast cancer imaging.

Multi-channel imaging data is a prevalent data format in scientific fields such as astronomy and biology. The structured information and the high dimensionality of these 3-D tensor data makes the analysis an intriguing but challenging topic for statisticians and practitioners. The low-rank scalar-on-tensor regression model, in particular, has received widespread attention and has been re-formulated as a tensor Gaussian Process (Tensor-GP) model with multi-linear kernel in Yu et al. (2018). In this paper, we extend the Tensor-GP model by integrating a dimensionality reduction technique, called tensor contraction, with a Tensor-GP for a scalar-on-tensor regression task with multi-channel imaging data. This is motivated by the solar flare forecasting problem with high dimensional multi-channel imaging data. We first estimate a latent, reduced-size tensor for each data tensor and then apply a multi-linear Tensor-GP on the latent tensor data for prediction. We introduce an anisotropic total-variation regularization when conducting the tensor contraction to obtain a sparse and smooth latent tensor. We then propose an alternating proximal gradient descent algorithm for estimation. We validate our approach via extensive simulation studies and applying it to the solar flare forecasting problem.

Curating a large scale medical imaging dataset for machine learning applications is both time consuming and expensive. Balancing the workload between model development, data collection and annotations is difficult for machine learning practitioners, especially under time constraints. Causal analysis is often used in medicine and economics to gain insights about the effects of actions and policies. In this paper we explore the effect of dataset interventions on the output of image classification models. Through a causal approach we investigate the effects of the quantity and type of data we need to incorporate in a dataset to achieve better performance for specific subtasks. The main goal of this paper is to highlight the potential of causal analysis as a tool for resource optimization for developing medical imaging ML applications. We explore this concept with a synthetic dataset and an exemplary use-case for Diabetic Retinopathy image analysis.

To generate evidence regarding the safety and efficacy of artificial intelligence (AI) enabled medical devices, AI models need to be evaluated on a diverse population of patient cases, some of which may not be readily available. We propose an evaluation approach for testing medical imaging AI models that relies on in silico imaging pipelines in which stochastic digital models of human anatomy (in object space) with and without pathology are imaged using a digital replica imaging acquisition system to generate realistic synthetic image datasets. Here, we release M-SYNTH, a dataset of cohorts with four breast fibroglandular density distributions imaged at different exposure levels using Monte Carlo x-ray simulations with the publicly available Virtual Imaging Clinical Trial for Regulatory Evaluation (VICTRE) toolkit. We utilize the synthetic dataset to analyze AI model performance and find that model performance decreases with increasing breast density and increases with higher mass density, as expected. As exposure levels decrease, AI model performance drops with the highest performance achieved at exposure levels lower than the nominal recommended dose for the breast type.

Foundation models, often pre-trained with large-scale data, have achieved paramount success in jump-starting various vision and language applications. Recent advances further enable adapting foundation models in downstream tasks efficiently using only a few training samples, e.g., in-context learning. Yet, the application of such learning paradigms in medical image analysis remains scarce due to the shortage of publicly accessible data and benchmarks. In this paper, we aim at approaches adapting the foundation models for medical image classification and present a novel dataset and benchmark for the evaluation, i.e., examining the overall performance of accommodating the large-scale foundation models downstream on a set of diverse real-world clinical tasks. We collect five sets of medical imaging data from multiple institutes targeting a variety of real-world clinical tasks (22,349 images in total), i.e., thoracic diseases screening in X-rays, pathological lesion tissue screening, lesion detection in endoscopy images, neonatal jaundice evaluation, and diabetic retinopathy grading. Results of multiple baseline methods are demonstrated using the proposed dataset from both accuracy and cost-effective perspectives.

Small sample sizes are common in many disciplines, which necessitates pooling roughly similar datasets across multiple institutions to study weak but relevant associations between images and disease outcomes. Such data often manifest shift/imbalance in covariates (i.e., secondary non-imaging data). Controlling for such nuisance variables is common within standard statistical analysis, but the ideas do not directly apply to overparameterized models. Consequently, recent work has shown how strategies from invariant representation learning provides a meaningful starting point, but the current repertoire of methods is limited to accounting for shifts/imbalances in just a couple of covariates at a time. In this paper, we show how viewing this problem from the perspective of Category theory provides a simple and effective solution that completely avoids elaborate multi-stage training pipelines that would otherwise be needed. We show the effectiveness of this approach via extensive experiments on real datasets. Further, we discuss how this style of formulation offers a unified perspective on at least 5+ distinct problem settings, from self-supervised learning to matching problems in 3D reconstruction.

The morphometry of a kidney tumor revealed by contrast-enhanced Computed Tomography (CT) imaging is an important factor in clinical decision making surrounding the lesion's diagnosis and treatment. Quantitative study of the relationship between kidney tumor morphology and clinical outcomes is difficult due to data scarcity and the laborious nature of manually quantifying imaging predictors. Automatic semantic segmentation of kidneys and kidney tumors is a promising tool towards automatically quantifying a wide array of morphometric features, but no sizeable annotated dataset is currently available to train models for this task. We present the KiTS19 challenge dataset: A collection of multi-phase CT imaging, segmentation masks, and comprehensive clinical outcomes for 300 patients who underwent nephrectomy for kidney tumors at our center between 2010 and 2018. 210 (70%) of these patients were selected at random as the training set for the 2019 MICCAI KiTS Kidney Tumor Segmentation Challenge and have been released publicly. With the presence of clinical context and surgical outcomes, this data can serve not only for benchmarking semantic segmentation models, but also for developing and studying biomarkers which make use of the imaging and semantic segmentation masks.

High-resolution imaging is crucial for enhancing visual clarity and enabling precise computer-assisted guidance in minimally invasive surgery (MIS). Despite the increasing adoption of 4K endoscopic systems, there remains a significant gap in publicly available native 4K datasets tailored specifically for robotic-assisted MIS. We introduce SurgiSR4K, the first publicly accessible surgical imaging and video dataset captured at a native 4K resolution, representing realistic conditions of robotic-assisted procedures. SurgiSR4K comprises diverse visual scenarios including specular reflections, tool occlusions, bleeding, and soft tissue deformations, meticulously designed to reflect common challenges faced during laparoscopic and robotic surgeries. This dataset opens up possibilities for a broad range of computer vision tasks that might benefit from high resolution data, such as super resolution (SR), smoke removal, surgical instrument detection, 3D tissue reconstruction, monocular depth estimation, instance segmentation, novel view synthesis, and vision-language model (VLM) development. SurgiSR4K provides a robust foundation for advancing research in high-resolution surgical imaging and fosters the development of intelligent imaging technologies aimed at enhancing performance, safety, and usability in image-guided robotic surgeries.

Current methods for performing 3D reconstruction and novel view synthesis (NVS) in ultrasound imaging data often face severe artifacts when training NeRF-based approaches. The artifacts produced by current approaches differ from NeRF floaters in general scenes because of the unique nature of ultrasound capture. Furthermore, existing models fail to produce reasonable 3D reconstructions when ultrasound data is captured or obtained casually in uncontrolled environments, which is common in clinical settings. Consequently, existing reconstruction and NVS methods struggle to handle ultrasound motion, fail to capture intricate details, and cannot model transparent and reflective surfaces. In this work, we introduced NeRF-US, which incorporates 3D-geometry guidance for border probability and scattering density into NeRF training, while also utilizing ultrasound-specific rendering over traditional volume rendering. These 3D priors are learned through a diffusion model. Through experiments conducted on our new "Ultrasound in the Wild" dataset, we observed accurate, clinically plausible, artifact-free reconstructions.

Glaucoma is the number one cause of irreversible blindness globally. A major challenge for accurate glaucoma detection and progression forecasting is the bottleneck of limited labeled patients with the state-of-the-art (SOTA) 3D retinal imaging data of optical coherence tomography (OCT). To address the data scarcity issue, this paper proposes two solutions. First, we develop a novel generalization-reinforced semi-supervised learning (SSL) model called pseudo supervisor to optimally utilize unlabeled data. Compared with SOTA models, the proposed pseudo supervisor optimizes the policy of predicting pseudo labels with unlabeled samples to improve empirical generalization. Our pseudo supervisor model is evaluated with two clinical tasks consisting of glaucoma detection and progression forecasting. The progression forecasting task is evaluated both unimodally and multimodally. Our pseudo supervisor model demonstrates superior performance than SOTA SSL comparison models. Moreover, our model also achieves the best results on the publicly available LAG fundus dataset. Second, we introduce the Harvard Glaucoma Detection and Progression (Harvard-GDP) Dataset, a multimodal multitask dataset that includes data from 1,000 patients with OCT imaging data, as well as labels for glaucoma detection and progression. This is the largest glaucoma detection dataset with 3D OCT imaging data and the first glaucoma progression forecasting dataset that is publicly available. Detailed sex and racial analysis are provided, which can be used by interested researchers for fairness learning studies. Our released dataset is benchmarked with several SOTA supervised CNN and transformer deep learning models. The dataset and code are made publicly available via https://ophai.hms.harvard.edu/datasets/harvard-gdp1000.

Semantic segmentation of medical images aims to associate a pixel with a label in a medical image without human initialization. The success of semantic segmentation algorithms is contingent on the availability of high-quality imaging data with corresponding labels provided by experts. We sought to create a large collection of annotated medical image datasets of various clinically relevant anatomies available under open source license to facilitate the development of semantic segmentation algorithms. Such a resource would allow: 1) objective assessment of general-purpose segmentation methods through comprehensive benchmarking and 2) open and free access to medical image data for any researcher interested in the problem domain. Through a multi-institutional effort, we generated a large, curated dataset representative of several highly variable segmentation tasks that was used in a crowd-sourced challenge - the Medical Segmentation Decathlon held during the 2018 Medical Image Computing and Computer Aided Interventions Conference in Granada, Spain. Here, we describe these ten labeled image datasets so that these data may be effectively reused by the research community.

Nematode worms are one of most abundant metazoan groups on the earth, occupying diverse ecological niches. Accurate recognition or identification of nematodes are of great importance for pest control, soil ecology, bio-geography, habitat conservation and against climate changes. Computer vision and image processing have witnessed a few successes in species recognition of nematodes; however, it is still in great demand. In this paper, we identify two main bottlenecks: (1) the lack of a publicly available imaging dataset for diverse species of nematodes (especially the species only found in natural environment) which requires considerable human resources in field work and experts in taxonomy, and (2) the lack of a standard benchmark of state-of-the-art deep learning techniques on this dataset which demands the discipline background in computer science. With these in mind, we propose an image dataset consisting of diverse nematodes (both laboratory cultured and naturally isolated), which, to our knowledge, is the first time in the community. We further set up a species recognition benchmark by employing state-of-the-art deep learning networks on this dataset. We discuss the experimental results, compare the recognition accuracy of different networks, and show the challenges of our dataset. We make our dataset publicly available at: https://github.com/xuequanlu/I-Nema

Developing accurate machine learning models for oncology requires large-scale, high-quality multimodal datasets. However, creating such datasets remains challenging due to the complexity and heterogeneity of medical data. To address this challenge, we introduce HoneyBee, a scalable modular framework for building multimodal oncology datasets that leverages foundational models to generate representative embeddings. HoneyBee integrates various data modalities, including clinical records, imaging data, and patient outcomes. It employs data preprocessing techniques and transformer-based architectures to generate embeddings that capture the essential features and relationships within the raw medical data. The generated embeddings are stored in a structured format using Hugging Face datasets and PyTorch dataloaders for accessibility. Vector databases enable efficient querying and retrieval for machine learning applications. We demonstrate the effectiveness of HoneyBee through experiments assessing the quality and representativeness of the embeddings. The framework is designed to be extensible to other medical domains and aims to accelerate oncology research by providing high-quality, machine learning-ready datasets. HoneyBee is an ongoing open-source effort, and the code, datasets, and models are available at the project repository.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

Deep neural networks are often applied to medical images to automate the problem of medical diagnosis. However, a more clinically relevant question that practitioners usually face is how to predict the future trajectory of a disease. Current methods for prognosis or disease trajectory forecasting often require domain knowledge and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many prediction problem. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner -- we predict prognosis with two transformer-based components that share information with each other. The first transformer in this framework aims to analyze the imaging data, and the second one leverages its internal states as inputs, also fusing them with auxiliary clinical data. The temporal nature of the problem is modeled within the transformer states, allowing us to treat the forecasting problem as a multi-task classification, for which we propose a novel loss. We show the effectiveness of our approach in predicting the development of structural knee osteoarthritis changes and forecasting Alzheimer's disease clinical status directly from raw multi-modal data. The proposed method outperforms multiple state-of-the-art baselines with respect to performance and calibration, both of which are needed for real-world applications. An open-source implementation of our method is made publicly available at https://github.com/Oulu-IMEDS/CLIMATv2.

We present a multilinear statistical model of the human tongue that captures anatomical and tongue pose related shape variations separately. The model is derived from 3D magnetic resonance imaging data of 11 speakers sustaining speech related vocal tract configurations. The extraction is performed by using a minimally supervised method that uses as basis an image segmentation approach and a template fitting technique. Furthermore, it uses image denoising to deal with possibly corrupt data, palate surface information reconstruction to handle palatal tongue contacts, and a bootstrap strategy to refine the obtained shapes. Our evaluation concludes that limiting the degrees of freedom for the anatomical and speech related variations to 5 and 4, respectively, produces a model that can reliably register unknown data while avoiding overfitting effects. Furthermore, we show that it can be used to generate a plausible tongue animation by tracking sparse motion capture data.

One of the key impediments for developing and assessing robust medical imaging algorithms is limited access to large-scale datasets with suitable annotations. Synthetic data generated with plausible physical and biological constraints may address some of these data limitations. We propose the use of physics simulations to generate synthetic images with pixel-level segmentation annotations, which are notoriously difficult to obtain. Specifically, we apply this approach to breast imaging analysis and release T-SYNTH, a large-scale open-source dataset of paired 2D digital mammography (DM) and 3D digital breast tomosynthesis (DBT) images. Our initial experimental results indicate that T-SYNTH images show promise for augmenting limited real patient datasets for detection tasks in DM and DBT. Our data and code are publicly available at https://github.com/DIDSR/tsynth-release.

This paper investigates discrepancies in how neural networks learn from different imaging domains, which are commonly overlooked when adopting computer vision techniques from the domain of natural images to other specialized domains such as medical images. Recent works have found that the generalization error of a trained network typically increases with the intrinsic dimension (d_{data}) of its training set. Yet, the steepness of this relationship varies significantly between medical (radiological) and natural imaging domains, with no existing theoretical explanation. We address this gap in knowledge by establishing and empirically validating a generalization scaling law with respect to d_{data}, and propose that the substantial scaling discrepancy between the two considered domains may be at least partially attributed to the higher intrinsic ``label sharpness'' (K_F) of medical imaging datasets, a metric which we propose. Next, we demonstrate an additional benefit of measuring the label sharpness of a training set: it is negatively correlated with the trained model's adversarial robustness, which notably leads to models for medical images having a substantially higher vulnerability to adversarial attack. Finally, we extend our d_{data} formalism to the related metric of learned representation intrinsic dimension (d_{repr}), derive a generalization scaling law with respect to d_{repr}, and show that d_{data} serves as an upper bound for d_{repr}. Our theoretical results are supported by thorough experiments with six models and eleven natural and medical imaging datasets over a range of training set sizes. Our findings offer insights into the influence of intrinsic dataset properties on generalization, representation learning, and robustness in deep neural networks. Code link: https://github.com/mazurowski-lab/intrinsic-properties

Failure of machine learning models to generalize to new data is a core problem limiting the reliability of AI systems, partly due to the lack of simple and robust methods for comparing new data to the original training dataset. We propose a standardized approach for assessing data similarity in a model-agnostic manner by constructing a supervised autoencoder for generalizability estimation (SAGE). We compare points in a low-dimensional embedded latent space, defining empirical probability measures for k-Nearest Neighbors (kNN) distance, reconstruction of inputs and task-based performance. As proof of concept for classification tasks, we use MNIST and CIFAR-10 to demonstrate how an ensemble output probability score can separate deformed images from a mixture of typical test examples, and how this SAGE score is robust to transformations of increasing severity. As further proof of concept, we extend this approach to a regression task using non-imaging data (UCI Abalone). In all cases, we show that out-of-the-box model performance increases after SAGE score filtering, even when applied to data from the model's own training and test datasets. Our out-of-distribution scoring method can be introduced during several steps of model construction and assessment, leading to future improvements in responsible deep learning implementation.

Single cell analysis of human skeletal muscle (SM) tissue cross-sections is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be automatic and precise. Biomedical scientists in this field currently rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to fine-tune segmentation. We believe that fully automated, precise, reproducible segmentation is possible by training ML models. However, in this important biomedical domain, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human SM tissue cross-sections from both healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include > 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibre segmentations, annotating reasons for rejecting low quality myofibres and low quality regions in SM tissue images, making these annotations completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

Stroke remains a leading cause of global morbidity and mortality, placing a heavy socioeconomic burden. Over the past decade, advances in endovascular reperfusion therapy and the use of CT and MRI imaging for treatment guidance have significantly improved patient outcomes and are now standard in clinical practice. To develop machine learning algorithms that can extract meaningful and reproducible models of brain function for both clinical and research purposes from stroke images - particularly for lesion identification, brain health quantification, and prognosis - large, diverse, and well-annotated public datasets are essential. While only a few datasets with (sub-)acute stroke data were previously available, several large, high-quality datasets have recently been made publicly accessible. However, these existing datasets include only MRI data. In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome. The dataset includes a training dataset of n = 150 and a test dataset of n = 100 scans. Training data is publicly available, while test data will be used exclusively for model validation. We are making this dataset available as part of the 2024 edition of the Ischemic Stroke Lesion Segmentation (ISLES) challenge (https://www.isles-challenge.org/), which continuously aims to establish benchmark methods for acute and sub-acute ischemic stroke lesion segmentation, aiding in creating open stroke imaging datasets and evaluating cutting-edge image processing algorithms.

Addressing the critical theme of recycling electronic waste (E-waste), this contribution is dedicated to developing advanced automated data processing pipelines as a basis for decision-making and process control. Aligning with the broader goals of the circular economy and the United Nations (UN) Sustainable Development Goals (SDG), our work leverages non-invasive analysis methods utilizing RGB and hyperspectral imaging data to provide both quantitative and qualitative insights into the E-waste stream composition for optimizing recycling efficiency. In this paper, we introduce 'PCB-Vision'; a pioneering RGB-hyperspectral printed circuit board (PCB) benchmark dataset, comprising 53 RGB images of high spatial resolution paired with their corresponding high spectral resolution hyperspectral data cubes in the visible and near-infrared (VNIR) range. Grounded in open science principles, our dataset provides a comprehensive resource for researchers through high-quality ground truths, focusing on three primary PCB components: integrated circuits (IC), capacitors, and connectors. We provide extensive statistical investigations on the proposed dataset together with the performance of several state-of-the-art (SOTA) models, including U-Net, Attention U-Net, Residual U-Net, LinkNet, and DeepLabv3+. By openly sharing this multi-scene benchmark dataset along with the baseline codes, we hope to foster transparent, traceable, and comparable developments of advanced data processing across various scientific communities, including, but not limited to, computer vision and remote sensing. Emphasizing our commitment to supporting a collaborative and inclusive scientific community, all materials, including code, data, ground truth, and masks, will be accessible at https://github.com/hifexplo/PCBVision.

Medical images and radiology reports are crucial for diagnosing medical conditions, highlighting the importance of quantitative analysis for clinical decision-making. However, the diversity and cross-source heterogeneity of these data challenge the generalizability of current data-mining methods. Multimodal large language models (MLLMs) have recently transformed many domains, significantly affecting the medical field. Notably, Gemini-Vision-series (Gemini) and GPT-4-series (GPT-4) models have epitomized a paradigm shift in Artificial General Intelligence (AGI) for computer vision, showcasing their potential in the biomedical domain. In this study, we evaluated the performance of the Gemini, GPT-4, and 4 popular large models for an exhaustive evaluation across 14 medical imaging datasets, including 5 medical imaging categories (dermatology, radiology, dentistry, ophthalmology, and endoscopy), and 3 radiology report datasets. The investigated tasks encompass disease classification, lesion segmentation, anatomical localization, disease diagnosis, report generation, and lesion detection. Our experimental results demonstrated that Gemini-series models excelled in report generation and lesion detection but faces challenges in disease classification and anatomical localization. Conversely, GPT-series models exhibited proficiency in lesion segmentation and anatomical localization but encountered difficulties in disease diagnosis and lesion detection. Additionally, both the Gemini series and GPT series contain models that have demonstrated commendable generation efficiency. While both models hold promise in reducing physician workload, alleviating pressure on limited healthcare resources, and fostering collaboration between clinical practitioners and artificial intelligence technologies, substantial enhancements and comprehensive validations remain imperative before clinical deployment.

Recently, intelligent analysis of lung nodules with the assistant of computer aided detection (CAD) techniques can improve the accuracy rate of lung cancer diagnosis. However, existing CAD systems and pulmonary datasets mainly focus on Computed Tomography (CT) images from one single period, while ignoring the cross spatio-temporal features associated with the progression of nodules contained in imaging data from various captured periods of lung cancer. If the evolution patterns of nodules across various periods in the patients' CT sequences can be explored, it will play a crucial role in guiding the precise screening identification of lung cancer. Therefore, a cross spatio-temporal lung nodule dataset with pathological information for nodule identification and diagnosis is constructed, which contains 328 CT sequences and 362 annotated nodules from 109 patients. This comprehensive database is intended to drive research in the field of CAD towards more practical and robust methods, and also contribute to the further exploration of precision medicine related field. To ensure patient confidentiality, we have removed sensitive information from the dataset.

Prenatal ultrasound imaging is the first-choice modality to assess fetal health. Medical image datasets for AI and ML methods must be diverse (i.e. diagnoses, diseases, pathologies, scanners, demographics, etc), however there are few public ultrasound fetal imaging datasets due to insufficient amounts of clinical data, patient privacy, rare occurrence of abnormalities in general practice, and limited experts for data collection and validation. To address such data scarcity, we proposed generative adversarial networks (GAN)-based models, diffusion-super-resolution-GAN and transformer-based-GAN, to synthesise images of fetal ultrasound brain planes from one public dataset. We reported that GAN-based methods can generate 256x256 pixel size of fetal ultrasound trans-cerebellum brain image plane with stable training losses, resulting in lower FID values for diffusion-super-resolution-GAN (average 7.04 and lower FID 5.09 at epoch 10) than the FID values of transformer-based-GAN (average 36.02 and lower 28.93 at epoch 60). The results of this work illustrate the potential of GAN-based methods to synthesise realistic high-resolution ultrasound images, leading to future work with other fetal brain planes, anatomies, devices and the need of a pool of experts to evaluate synthesised images. Code, data and other resources to reproduce this work are available at https://github.com/budai4medtech/midl2023.

Multimodal large language models (MLLMs) have recently demonstrated remarkable reasoning abilities with reinforcement learning paradigm. Although several multimodal reasoning models have been explored in the medical domain, most of them focus exclusively on basic reasoning, which refers to shallow inference based on visual feature matching. However, real-world clinical diagnosis extends beyond basic reasoning, demanding reasoning processes that integrate heterogeneous clinical information (such as chief complaints and medical history) with multimodal medical imaging data. To bridge this gap, we introduce MM-Retinal-Reason, the first ophthalmic multimodal dataset with the full spectrum of perception and reasoning. It encompasses both basic reasoning tasks and complex reasoning tasks, aiming to enhance visual-centric fundamental reasoning capabilities and emulate realistic clinical thinking patterns. Building upon MM-Retinal-Reason, we propose OphthaReason, the first ophthalmology-specific multimodal reasoning model with step-by-step reasoning traces. To enable flexible adaptation to both basic and complex reasoning tasks, we specifically design a novel method called Uncertainty-Aware Dynamic Thinking (UADT), which estimates sample-level uncertainty via entropy and dynamically modulates the model's exploration depth using a shaped advantage mechanism. Comprehensive experiments demonstrate that our model achieves state-of-the-art performance on both basic and complex reasoning tasks, outperforming general-purpose MLLMs, medical MLLMs, RL-based medical MLLMs, and ophthalmic MLLMs by at least 24.92\%, 15.00\%, 21.20\%, and 17.66\%. Project Page: https://github.com/lxirich/OphthaReason{link}.

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.

Machine learning models for medical image analysis often suffer from poor performance on important subsets of a population that are not identified during training or testing. For example, overall performance of a cancer detection model may be high, but the model still consistently misses a rare but aggressive cancer subtype. We refer to this problem as hidden stratification, and observe that it results from incompletely describing the meaningful variation in a dataset. While hidden stratification can substantially reduce the clinical efficacy of machine learning models, its effects remain difficult to measure. In this work, we assess the utility of several possible techniques for measuring and describing hidden stratification effects, and characterize these effects on multiple medical imaging datasets. We find evidence that hidden stratification can occur in unidentified imaging subsets with low prevalence, low label quality, subtle distinguishing features, or spurious correlates, and that it can result in relative performance differences of over 20% on clinically important subsets. Finally, we explore the clinical implications of our findings, and suggest that evaluation of hidden stratification should be a critical component of any machine learning deployment in medical imaging.

Limitations on bandwidth and power consumption impose strict bounds on data rates of diagnostic imaging systems. Consequently, the design of suitable (i.e. task- and data-aware) compression and reconstruction techniques has attracted considerable attention in recent years. Compressed sensing emerged as a popular framework for sparse signal reconstruction from a small set of compressed measurements. However, typical compressed sensing designs measure a (non)linearly weighted combination of all input signal elements, which poses practical challenges. These designs are also not necessarily task-optimal. In addition, real-time recovery is hampered by the iterative and time-consuming nature of sparse recovery algorithms. Recently, deep learning methods have shown promise for fast recovery from compressed measurements, but the design of adequate and practical sensing strategies remains a challenge. Here, we propose a deep learning solution termed Deep Probabilistic Sub-sampling (DPS), that learns a task-driven sub-sampling pattern, while jointly training a subsequent task model. Once learned, the task-based sub-sampling patterns are fixed and straightforwardly implementable, e.g. by non-uniform analog-to-digital conversion, sparse array design, or slow-time ultrasound pulsing schemes. The effectiveness of our framework is demonstrated in-silico for sparse signal recovery from partial Fourier measurements, and in-vivo for both anatomical image and tissue-motion (Doppler) reconstruction from sub-sampled medical ultrasound imaging data.

We propose a novel neural deformable model (NDM) targeting at the reconstruction and modeling of 3D bi-ventricular shape of the heart from 2D sparse cardiac magnetic resonance (CMR) imaging data. We model the bi-ventricular shape using blended deformable superquadrics, which are parameterized by a set of geometric parameter functions and are capable of deforming globally and locally. While global geometric parameter functions and deformations capture gross shape features from visual data, local deformations, parameterized as neural diffeomorphic point flows, can be learned to recover the detailed heart shape.Different from iterative optimization methods used in conventional deformable model formulations, NDMs can be trained to learn such geometric parameter functions, global and local deformations from a shape distribution manifold. Our NDM can learn to densify a sparse cardiac point cloud with arbitrary scales and generate high-quality triangular meshes automatically. It also enables the implicit learning of dense correspondences among different heart shape instances for accurate cardiac shape registration. Furthermore, the parameters of NDM are intuitive, and can be used by a physician without sophisticated post-processing. Experimental results on a large CMR dataset demonstrate the improved performance of NDM over conventional methods.

Multimodal models trained on large natural image-text pair datasets have exhibited astounding abilities in generating high-quality images. Medical imaging data is fundamentally different to natural images, and the language used to succinctly capture relevant details in medical data uses a different, narrow but semantically rich, domain-specific vocabulary. Not surprisingly, multi-modal models trained on natural image-text pairs do not tend to generalize well to the medical domain. Developing generative imaging models faithfully representing medical concepts while providing compositional diversity could mitigate the existing paucity of high-quality, annotated medical imaging datasets. In this work, we develop a strategy to overcome the large natural-medical distributional shift by adapting a pre-trained latent diffusion model on a corpus of publicly available chest x-rays (CXR) and their corresponding radiology (text) reports. We investigate the model's ability to generate high-fidelity, diverse synthetic CXR conditioned on text prompts. We assess the model outputs quantitatively using image quality metrics, and evaluate image quality and text-image alignment by human domain experts. We present evidence that the resulting model (RoentGen) is able to create visually convincing, diverse synthetic CXR images, and that the output can be controlled to a new extent by using free-form text prompts including radiology-specific language. Fine-tuning this model on a fixed training set and using it as a data augmentation method, we measure a 5% improvement of a classifier trained jointly on synthetic and real images, and a 3% improvement when trained on a larger but purely synthetic training set. Finally, we observe that this fine-tuning distills in-domain knowledge in the text-encoder and can improve its representation capabilities of certain diseases like pneumothorax by 25%.

Biomedical imaging datasets are often small and biased, meaning that real-world performance of predictive models can be substantially lower than expected from internal testing. This work proposes using generative image editing to simulate dataset shifts and diagnose failure modes of biomedical vision models; this can be used in advance of deployment to assess readiness, potentially reducing cost and patient harm. Existing editing methods can produce undesirable changes, with spurious correlations learned due to the co-occurrence of disease and treatment interventions, limiting practical applicability. To address this, we train a text-to-image diffusion model on multiple chest X-ray datasets and introduce a new editing method RadEdit that uses multiple masks, if present, to constrain changes and ensure consistency in the edited images. We consider three types of dataset shifts: acquisition shift, manifestation shift, and population shift, and demonstrate that our approach can diagnose failures and quantify model robustness without additional data collection, complementing more qualitative tools for explainable AI.

Robust and accurate detection and segmentation of heterogenous tumors appearing in different anatomical organs with supervised methods require large-scale labeled datasets covering all possible types of diseases. Due to the unavailability of such rich datasets and the high cost of annotations, unsupervised anomaly detection (UAD) methods have been developed aiming to detect the pathologies as deviation from the normality by utilizing the unlabeled healthy image data. However, developed UAD models are often trained with an incomplete distribution of healthy anatomies and have difficulties in preserving anatomical constraints. This work intends to, first, propose a robust inpainting model to learn the details of healthy anatomies and reconstruct high-resolution images by preserving anatomical constraints. Second, we propose an autoinpainting pipeline to automatically detect tumors, replace their appearance with the learned healthy anatomies, and based on that segment the tumoral volumes in a purely unsupervised fashion. Three imaging datasets, including PET, CT, and PET-CT scans of lung tumors and head and neck tumors, are studied as benchmarks for evaluation. Experimental results demonstrate the significant superiority of the proposed method over a wide range of state-of-the-art UAD methods. Moreover, the unsupervised method we propose produces comparable results to a robust supervised segmentation method when applied to multimodal images.

Segment Anything Model (SAM) has gained significant attention because of its ability to segment a variety of objects in images given a prompt. The recently developed SAM 2 has extended this ability to video inputs. This opens an opportunity to apply SAM to 3D images, one of the fundamental tasks in the medical imaging field. In this paper, we provide an extensive evaluation of SAM 2's ability to segment both 2D and 3D medical images. We collect 18 medical imaging datasets, including common 3D modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET) as well as 2D modalities such as X-ray and ultrasound. We consider two evaluation pipelines of SAM 2: (1) multi-frame 3D segmentation, where prompts are provided to one or multiple slice(s) selected from the volume, and (2) single-frame 2D segmentation, where prompts are provided to each slice. The former is only applicable to 3D modalities, while the latter applies to both 2D and 3D modalities. We learn that SAM 2 exhibits similar performance as SAM under single-frame 2D segmentation, and has variable performance under multi-frame 3D segmentation depending on the choices of slices to annotate, the direction of the propagation, the predictions utilized during the propagation, etc.

Large medical imaging datasets can be cheaply and quickly annotated with low-confidence, weak labels (e.g., radiological scores). Access to high-confidence labels, such as histology-based diagnoses, is rare and costly. Pretraining strategies, like contrastive learning (CL) methods, can leverage unlabeled or weakly-annotated datasets. These methods typically require large batch sizes, which poses a difficulty in the case of large 3D images at full resolution, due to limited GPU memory. Nevertheless, volumetric positional information about the spatial context of each 2D slice can be very important for some medical applications. In this work, we propose an efficient weakly-supervised positional (WSP) contrastive learning strategy where we integrate both the spatial context of each 2D slice and a weak label via a generic kernel-based loss function. We illustrate our method on cirrhosis prediction using a large volume of weakly-labeled images, namely radiological low-confidence annotations, and small strongly-labeled (i.e., high-confidence) datasets. The proposed model improves the classification AUC by 5% with respect to a baseline model on our internal dataset, and by 26% on the public LIHC dataset from the Cancer Genome Atlas. The code is available at: https://github.com/Guerbet-AI/wsp-contrastive.

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

We focus on the source-free domain adaptive object detection (SF-DAOD) problem when source data is unavailable during adaptation and the model must adapt to an unlabeled target domain. The majority of approaches for the problem employ a self-supervised approach using a student-teacher (ST) framework where pseudo-labels are generated via a source-pretrained model for further fine-tuning. We observe that the performance of a student model often degrades drastically, due to the collapse of the teacher model, primarily caused by high noise in pseudo-labels, resulting from domain bias, discrepancies, and a significant domain shift across domains. To obtain reliable pseudo-labels, we propose a Target-based Iterative Query-Token Adversarial Network (TITAN), which separates the target images into two subsets: those similar to the source (easy) and those dissimilar (hard). We propose a strategy to estimate variance to partition the target domain. This approach leverages the insight that higher detection variances correspond to higher recall and greater similarity to the source domain. Also, we incorporate query-token-based adversarial modules into a student-teacher baseline framework to reduce the domain gaps between two feature representations. Experiments conducted on four natural imaging datasets and two challenging medical datasets have substantiated the superior performance of TITAN compared to existing state-of-the-art (SOTA) methodologies. We report an mAP improvement of +22.7, +22.2, +21.1, and +3.7 percent over the current SOTA on C2F, C2B, S2C, and K2C benchmarks, respectively.

In response to the global need for efficient early diagnosis of Autism Spectrum Disorder (ASD), this paper bridges the gap between traditional, time-consuming diagnostic methods and potential automated solutions. We propose a multi-atlas deep ensemble network, MADE-for-ASD, that integrates multiple atlases of the brain's functional magnetic resonance imaging (fMRI) data through a weighted deep ensemble network. Our approach integrates demographic information into the prediction workflow, which enhances ASD diagnosis performance and offers a more holistic perspective on patient profiling. We experiment with the well-known publicly available ABIDE (Autism Brain Imaging Data Exchange) I dataset, consisting of resting state fMRI data from 17 different laboratories around the globe. Our proposed system achieves 75.20% accuracy on the entire dataset and 96.40% on a specific subset - both surpassing reported ASD diagnosis accuracy in ABIDE I fMRI studies. Specifically, our model improves by 4.4 percentage points over prior works on the same amount of data. The model exhibits a sensitivity of 82.90% and a specificity of 69.70% on the entire dataset, and 91.00% and 99.50%, respectively, on the specific subset. We leverage the F-score to pinpoint the top 10 ROI in ASD diagnosis, such as precuneus and anterior cingulate/ventromedial. The proposed system can potentially pave the way for more cost-effective, efficient and scalable strategies in ASD diagnosis. Codes and evaluations are publicly available at https://github.com/hasan-rakibul/MADE-for-ASD.

Autism spectrum disorder (ASD) is a prevalent psychiatric condition characterized by atypical cognitive, emotional, and social patterns. Timely and accurate diagnosis is crucial for effective interventions and improved outcomes in individuals with ASD. In this study, we propose a novel Multi-Atlas Enhanced Transformer framework, METAFormer, ASD classification. Our framework utilizes resting-state functional magnetic resonance imaging data from the ABIDE I dataset, comprising 406 ASD and 476 typical control (TC) subjects. METAFormer employs a multi-atlas approach, where flattened connectivity matrices from the AAL, CC200, and DOS160 atlases serve as input to the transformer encoder. Notably, we demonstrate that self-supervised pretraining, involving the reconstruction of masked values from the input, significantly enhances classification performance without the need for additional or separate training data. Through stratified cross-validation, we evaluate the proposed framework and show that it surpasses state-of-the-art performance on the ABIDE I dataset, with an average accuracy of 83.7% and an AUC-score of 0.832. The code for our framework is available at https://github.com/Lugges991/METAFormer

Knee Osteoarthritis (KOA) is a highly prevalent chronic musculoskeletal condition with no currently available treatment. The manifestation of KOA is heterogeneous and prediction of its progression is challenging. Current literature suggests that the use of multi-modal data and advanced modeling methods, such as the ones based on Deep Learning, has promise in tackling this challenge. To date, however, the evidence on the efficacy of this approach is limited. In this study, we leveraged recent advances in Deep Learning and, using a Transformer approach, developed a unified framework for the multi-modal fusion of knee imaging data. Subsequently, we analyzed its performance across a range of scenarios by investigating multiple progression horizons -- from short-term to long-term. We report our findings using a large cohort (n=2421-3967) derived from the Osteoarthritis Initiative dataset. We show that structural knee MRI allows identifying radiographic KOA progressors on par with multi-modal fusion approaches, achieving an area under the ROC curve (ROC AUC) of 0.70-0.76 and Average Precision (AP) of 0.15-0.54 in 2-8 year horizons. Progression within 1 year was better predicted with a multi-modal method using X-ray, structural, and compositional MR images -- ROC AUC of 0.76(0.04), AP of 0.13(0.04) -- or via clinical data. Our follow-up analysis generally shows that prediction from the imaging data is more accurate for post-traumatic subjects, and we further investigate which subject subgroups may benefit the most. The present study provides novel insights into multi-modal imaging of KOA and brings a unified data-driven framework for studying its progression in an end-to-end manner, providing new tools for the design of more efficient clinical trials. The source code of our framework and the pre-trained models are made publicly available.

Despite the ever-increasing interest in applying deep learning (DL) models to medical imaging, the typical scarcity and imbalance of medical datasets can severely impact the performance of DL models. The generation of synthetic data that might be freely shared without compromising patient privacy is a well-known technique for addressing these difficulties. Inpainting algorithms are a subset of DL generative models that can alter one or more regions of an input image while matching its surrounding context and, in certain cases, non-imaging input conditions. Although the majority of inpainting techniques for medical imaging data use generative adversarial networks (GANs), the performance of these algorithms is frequently suboptimal due to their limited output variety, a problem that is already well-known for GANs. Denoising diffusion probabilistic models (DDPMs) are a recently introduced family of generative networks that can generate results of comparable quality to GANs, but with diverse outputs. In this paper, we describe a DDPM to execute multiple inpainting tasks on 2D axial slices of brain MRI with various sequences, and present proof-of-concept examples of its performance in a variety of evaluation scenarios. Our model and a public online interface to try our tool are available at: https://github.com/Mayo-Radiology-Informatics-Lab/MBTI

In medical applications, deep learning methods are built to automate diagnostic tasks. However, a clinically relevant question that practitioners usually face, is how to predict the future trajectory of a disease (prognosis). Current methods for such a problem often require domain knowledge, and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many forecasting problem from multimodal data. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner, we model a prognosis prediction problem with two transformer-based components that share information between each other. The first block in this model aims to analyze the imaging data, and the second block leverages the internal representations of the first one as inputs, also fusing them with auxiliary patient data. We show the effectiveness of our method in predicting the development of structural knee osteoarthritis changes over time. Our results show that the proposed method outperforms the state-of-the-art baselines in terms of various performance metrics. In addition, we empirically show that the existence of the multi-agent transformers with depths of 2 is sufficient to achieve good performances. Our code is publicly available at https://github.com/MIPT-Oulu/CLIMAT.

Active learning promises to improve annotation efficiency by iteratively selecting the most important data to be annotated first. However, we uncover a striking contradiction to this promise: active learning fails to select data as efficiently as random selection at the first few choices. We identify this as the cold start problem in vision active learning, caused by a biased and outlier initial query. This paper seeks to address the cold start problem by exploiting the three advantages of contrastive learning: (1) no annotation is required; (2) label diversity is ensured by pseudo-labels to mitigate bias; (3) typical data is determined by contrastive features to reduce outliers. Experiments are conducted on CIFAR-10-LT and three medical imaging datasets (i.e. Colon Pathology, Abdominal CT, and Blood Cell Microscope). Our initial query not only significantly outperforms existing active querying strategies but also surpasses random selection by a large margin. We foresee our solution to the cold start problem as a simple yet strong baseline to choose the initial query for vision active learning. Code is available: https://github.com/c-liangyu/CSVAL

While the influence of galaxy clusters on galaxy evolution is relatively well-understood, the impact of the dynamical states of these clusters is less clear. This paper series explores how the dynamical state of galaxy clusters affects their galaxy populations' physical and morphological properties. The primary aim of this first paper is to evaluate the dynamical state of 87 massive (M_{500} geq 1.5 times 10^{14} M_{odot}) galaxy clusters at low redshifts (0.10 leq z leq 0.35). This will allow us to have a well-characterized sample for analyzing physical and morphological properties in our next work. We employ six dynamical state proxies utilizing optical and X-ray imaging data. Principal Component Analysis (PCA) is applied to integrate these proxies effectively, allowing for robust classification of galaxy clusters into relaxed, intermediate, and disturbed states based on their dynamical characteristics. The methodology successfully segregates the galaxy clusters into the three dynamical states. Examination of the galaxy distributions in optical wavelengths and gas distributions in X-ray further confirms the consistency of these classifications. The clusters' dynamical states are statistically distinguishable, providing a clear categorization for further analysis.

Although purely transformer-based architectures showed promising performance in many computer vision tasks, many hybrid models consisting of CNN and transformer blocks are introduced to fit more specialized tasks. Nevertheless, despite the performance gain of both pure and hybrid transformer-based architectures compared to CNNs in medical imaging segmentation, their high training cost and complexity make it challenging to use them in real scenarios. In this work, we propose simple architectures based on purely convolutional layers, and show that by just taking advantage of the attention map visualizations obtained from a self-supervised pretrained vision transformer network (e.g., DINO) one can outperform complex transformer-based networks with much less computation costs. The proposed architecture is composed of two encoder branches with the original image as input in one branch and the attention map visualizations of the same image from multiple self-attention heads from a pre-trained DINO model (as multiple channels) in the other branch. The results of our experiments on two publicly available medical imaging datasets show that the proposed pipeline outperforms U-Net and the state-of-the-art medical image segmentation models.

The scarcity of high-quality, labelled retinal imaging data, which presents a significant challenge in the development of machine learning models for ophthalmology, hinders progress in the field. Existing methods for synthesising Colour Fundus Photographs (CFPs) largely rely on predefined disease labels, which restricts their ability to generate images that reflect fine-grained anatomical variations, subtle disease stages, and diverse pathological features beyond coarse class categories. To overcome these challenges, we first introduce an innovative pipeline that creates a large-scale, captioned retinal dataset comprising 1.4 million entries, called RetinaLogos-1400k. Specifically, RetinaLogos-1400k uses the visual language model(VLM) to describe retinal conditions and key structures, such as optic disc configuration, vascular distribution, nerve fibre layers, and pathological features. Building on this dataset, we employ a novel three-step training framework, RetinaLogos, which enables fine-grained semantic control over retinal images and accurately captures different stages of disease progression, subtle anatomical variations, and specific lesion types. Through extensive experiments, our method demonstrates superior performance across multiple datasets, with 62.07% of text-driven synthetic CFPs indistinguishable from real ones by ophthalmologists. Moreover, the synthetic data improves accuracy by 5%-10% in diabetic retinopathy grading and glaucoma detection. Codes are available at https://github.com/uni-medical/retina-text2cfp.

Foundation models (FMs) have shown transformative potential in radiology by performing diverse, complex tasks across imaging modalities. Here, we developed CT-FM, a large-scale 3D image-based pre-trained model designed explicitly for various radiological tasks. CT-FM was pre-trained using 148,000 computed tomography (CT) scans from the Imaging Data Commons through label-agnostic contrastive learning. We evaluated CT-FM across four categories of tasks, namely, whole-body and tumor segmentation, head CT triage, medical image retrieval, and semantic understanding, showing superior performance against state-of-the-art models. Beyond quantitative success, CT-FM demonstrated the ability to cluster regions anatomically and identify similar anatomical and structural concepts across scans. Furthermore, it remained robust across test-retest settings and indicated reasonable salient regions attached to its embeddings. This study demonstrates the value of large-scale medical imaging foundation models and by open-sourcing the model weights, code, and data, aims to support more adaptable, reliable, and interpretable AI solutions in radiology.

The rapid advancement of Artificial Intelligence (AI) in biomedical imaging and radiotherapy is hindered by the limited availability of large imaging data repositories. With recent research and improvements in denoising diffusion probabilistic models (DDPM), high quality synthetic medical scans are now possible. Despite this, there is currently no way of generating multiple related images, such as a corresponding ground truth which can be used to train models, so synthetic scans are often manually annotated before use. This research introduces a novel architecture that is able to generate multiple, related PET-CT-tumour mask pairs using paired networks and conditional encoders. Our approach includes innovative, time step-controlled mechanisms and a `noise-seeding' strategy to improve DDPM sampling consistency. While our model requires a modified perceptual loss function to ensure accurate feature alignment we show generation of clearly aligned synthetic images and improvement in segmentation accuracy with generated images.

Segmenting medical images is critical to facilitating both patient diagnoses and quantitative research. A major limiting factor is the lack of labeled data, as obtaining expert annotations for each new set of imaging data and task can be labor intensive and inconsistent among annotators. We present CUTS, an unsupervised deep learning framework for medical image segmentation. CUTS operates in two stages. For each image, it produces an embedding map via intra-image contrastive learning and local patch reconstruction. Then, these embeddings are partitioned at dynamic granularity levels that correspond to the data topology. CUTS yields a series of coarse-to-fine-grained segmentations that highlight features at various granularities. We applied CUTS to retinal fundus images and two types of brain MRI images to delineate structures and patterns at different scales. When evaluated against predefined anatomical masks, CUTS improved the dice coefficient and Hausdorff distance by at least 10% compared to existing unsupervised methods. Finally, CUTS showed performance on par with Segment Anything Models (SAM, MedSAM, SAM-Med2D) pre-trained on gigantic labeled datasets.

The lottery ticket hypothesis has sparked the rapid development of pruning algorithms that aim to reduce the computational costs associated with deep learning during training and model deployment. Currently, such algorithms are primarily evaluated on imaging data, for which we lack ground truth information and thus the understanding of how sparse lottery tickets could be. To fill this gap, we develop a framework that allows us to plant and hide winning tickets with desirable properties in randomly initialized neural networks. To analyze the ability of state-of-the-art pruning to identify tickets of extreme sparsity, we design and hide such tickets solving four challenging tasks. In extensive experiments, we observe similar trends as in imaging studies, indicating that our framework can provide transferable insights into realistic problems. Additionally, we can now see beyond such relative trends and highlight limitations of current pruning methods. Based on our results, we conclude that the current limitations in ticket sparsity are likely of algorithmic rather than fundamental nature. We anticipate that comparisons to planted tickets will facilitate future developments of efficient pruning algorithms.

Training models with robust group fairness properties is crucial in ethically sensitive application areas such as medical diagnosis. Despite the growing body of work aiming to minimise demographic bias in AI, this problem remains challenging. A key reason for this challenge is the fairness generalisation gap: High-capacity deep learning models can fit all training data nearly perfectly, and thus also exhibit perfect fairness during training. In this case, bias emerges only during testing when generalisation performance differs across subgroups. This motivates us to take a bi-level optimisation perspective on fair learning: Optimising the learning strategy based on validation fairness. Specifically, we consider the highly effective workflow of adapting pre-trained models to downstream medical imaging tasks using parameter-efficient fine-tuning (PEFT) techniques. There is a trade-off between updating more parameters, enabling a better fit to the task of interest vs. fewer parameters, potentially reducing the generalisation gap. To manage this tradeoff, we propose FairTune, a framework to optimise the choice of PEFT parameters with respect to fairness. We demonstrate empirically that FairTune leads to improved fairness on a range of medical imaging datasets. The code is available at https://github.com/Raman1121/FairTune

Automated radiology report generation (RRG) aims to produce detailed textual reports from clinical imaging, such as computed tomography (CT) scans, to improve the accuracy and efficiency of diagnosis and provision of management advice. RRG is complicated by two key challenges: (1) inherent complexity in extracting relevant information from imaging data under resource constraints, and (2) difficulty in objectively evaluating discrepancies between model-generated and expert-written reports. To address these challenges, we propose mu^2LLM, a textbf{mu}ltiscale textbf{mu}ltimodal large language models for RRG tasks. The novel {mu}^2Tokenizer, as an intermediate layer, integrates multi-modal features from the multiscale visual tokenizer and the text tokenizer, then enhances report generation quality through direct preference optimization (DPO), guided by GREEN-RedLlama. Experimental results on four large CT image-report medical datasetdemonstrate that our method outperforms existing approaches, highlighting the potential of our fine-tuned mu^2LLMs on limited data for RRG tasks.

AI-assisted radiological interpretation is based on predominantly narrow, single-task models. This approach is impractical for covering the vast spectrum of imaging modalities, diseases, and radiological findings. Foundation models (FMs) hold the promise of broad generalization across modalities and in low-data settings. However, this potential has remained largely unrealized in radiology. We introduce Curia, a foundation model trained on the entire cross-sectional imaging output of a major hospital over several years, which to our knowledge is the largest such corpus of real-world data-encompassing 150,000 exams (130 TB). On a newly curated 19-task external validation benchmark, Curia accurately identifies organs, detects conditions like brain hemorrhages and myocardial infarctions, and predicts outcomes in tumor staging. Curia meets or surpasses the performance of radiologists and recent foundation models, and exhibits clinically significant emergent properties in cross-modality, and low-data regimes. To accelerate progress, we release our base model's weights at https://huggingface.co/raidium/curia.

Universal medical image segmentation models have emerged as a promising paradigm due to their strong generalizability across diverse tasks, showing great potential for a wide range of clinical applications. This potential has been partly driven by the success of general-purpose vision models such as the Segment Anything Model (SAM), which has inspired the development of various fine-tuned variants for medical segmentation tasks. However, fine-tuned variants like MedSAM are trained on comparatively limited medical imaging data that often suffers from heterogeneity, scarce annotations, and distributional shifts. These challenges limit their ability to generalize across a wide range of medical segmentation tasks. In this regard, we propose MedSAMix, a training-free model merging method that integrates the strengths of both generalist models (e.g., SAM) and specialist models (e.g., MedSAM) for medical image segmentation. In contrast to traditional model merging approaches that rely on manual configuration and often result in suboptimal outcomes, we propose a zero-order optimization method to automatically discover optimal layer-wise merging solutions. Furthermore, for clinical applications, we develop two regimes to meet the demand of domain-specificity and generalizability in different scenarios by single-task optimization and multi-objective optimization respectively. Extensive evaluations on 25 medical segmentation tasks demonstrate that MedSAMix effectively mitigates model bias and consistently improves performance in both domain-specific accuracy and generalization, achieving improvements of 6.67% on specialized tasks and 4.37% on multi-task evaluations.

Accurate prediction of major adverse cardiovascular events recurrence risk in acute myocardial infarction patients based on postoperative cardiac MRI and associated clinical notes is crucial for precision treatment and personalized intervention. Existing methods primarily focus on risk stratification capability while overlooking the need for intermediate robust reasoning and model interpretability in clinical practice. Moreover, end-to-end risk prediction using LLM/VLM faces significant challenges due to data limitations and modeling complexity. To bridge this gap, we propose CardioCoT, a novel two-stage hierarchical reasoning-enhanced survival analysis framework designed to enhance both model interpretability and predictive performance. In the first stage, we employ an evidence-augmented self-refinement mechanism to guide LLM/VLMs in generating robust hierarchical reasoning trajectories based on associated radiological findings. In the second stage, we integrate the reasoning trajectories with imaging data for risk model training and prediction. CardioCoT demonstrates superior performance in MACE recurrence risk prediction while providing interpretable reasoning processes, offering valuable insights for clinical decision-making.

Driven by the recent advances in deep learning methods and, in particular, by the development of modern self-supervised learning algorithms, increased interest and efforts have been devoted to build foundation models (FMs) for medical images. In this work, we present our scalable training pipeline for large pathology imaging data, and a comprehensive analysis of various hyperparameter choices and training techniques for building pathology FMs. We release and make publicly available the first batch of our pathology FMs (https://github.com/kaiko-ai/towards_large_pathology_fms) trained on open-access TCGA whole slide images, a commonly used collection of pathology images. The experimental evaluation shows that our models reach state-of-the-art performance on various patch-level downstream tasks, ranging from breast cancer subtyping to colorectal nuclear segmentation. Finally, to unify the evaluation approaches used in the field and to simplify future comparisons of different FMs, we present an open-source framework (https://github.com/kaiko-ai/eva) designed for the consistent evaluation of pathology FMs across various downstream tasks.

Artificial Intelligence (AI) has the potential to revolutionize diagnosis and segmentation in medical imaging. However, development and clinical implementation face multiple challenges including limited data availability, lack of generalizability, and the necessity to incorporate multi-modal data effectively. A foundation model, which is a large-scale pre-trained AI model, offers a versatile base that can be adapted to a variety of specific tasks and contexts. Here, we present a novel foundation model, VISION-MAE, specifically designed for medical imaging. Specifically, VISION-MAE is trained on a dataset of 2.5 million unlabeled images from various modalities (CT, MR, PET, X-rays, and ultrasound), using self-supervised learning techniques. It is then adapted to classification and segmentation tasks using explicit labels. VISION-MAE has high label efficiency, outperforming several benchmark models in both in-domain and out-of-domain applications, and achieves high performance even with reduced availability of labeled data. This model represents a significant advancement in medical imaging AI, offering a generalizable and robust solution for improving segmentation and classification tasks while reducing the data annotation workload.

Language-supervised pre-training has proven to be a valuable method for extracting semantically meaningful features from images, serving as a foundational element in multimodal systems within the computer vision and medical imaging domains. However, resulting features are limited by the information contained within the text. This is particularly problematic in medical imaging, where radiologists' written findings focus on specific observations; a challenge compounded by the scarcity of paired imaging-text data due to concerns over leakage of personal health information. In this work, we fundamentally challenge the prevailing reliance on language supervision for learning general purpose biomedical imaging encoders. We introduce RAD-DINO, a biomedical image encoder pre-trained solely on unimodal biomedical imaging data that obtains similar or greater performance than state-of-the-art biomedical language supervised models on a diverse range of benchmarks. Specifically, the quality of learned representations is evaluated on standard imaging tasks (classification and semantic segmentation), and a vision-language alignment task (text report generation from images). To further demonstrate the drawback of language supervision, we show that features from RAD-DINO correlate with other medical records (e.g., sex or age) better than language-supervised models, which are generally not mentioned in radiology reports. Finally, we conduct a series of ablations determining the factors in RAD-DINO's performance; notably, we observe that RAD-DINO's downstream performance scales well with the quantity and diversity of training data, demonstrating that image-only supervision is a scalable approach for training a foundational biomedical image encoder.

We use deep, mu_{r} lesssim 28,mag,arcsec^{-2}, r-band imaging from the Dark Energy Camera Legacy Survey (DECaLS) to search for past, or ongoing, merger activity in a sample of 282 Low Excitation Radio Galaxies (LERGs) at z<0.07. Our principle aim is to assess the the role of mergers in the evolution of LERGs. Exploiting the imaging depth, we classify tidal remnants around galaxies as both minor and major morphological disturbances for our LERG sample and 1,622 control galaxies matched in redshift, stellar mass, and environment. In groups and in the field, the LERG minor merger fraction is consistent with the control population. In galaxy clusters, 8.8 pm 2.9, % of LERGs show evidence of recent minor mergers in contrast to 23.0pm 2.0, % of controls. This sim 4 sigma deficit of minor mergers in cluster LERGs suggests these events may inhibit this type of nuclear activity for galaxies within the cluster environment. We observe a > 4sigma excess of major mergers in the LERGs with M_{*} lesssim 10^{11},M_{odot}, with 10 pm 1.5, % of these AGN involved in such large-scale interactions compared to 3.2 pm 0.4,% of control galaxies. This excess of major mergers in LERGs decreases with increasing stellar mass, vanishing by M_{*} > 10^{11.3},M_{odot}. These observations show that minor mergers do not fuel LERGs, and are consistent with typical LERGs being powered by accretion of matter from their halo. Where LERGs are associated with major mergers, these objects may evolve into more efficiently accreting active galactic nuclei as the merger progresses and more gas falls on to the central engine.

A major challenge in computational research in 3D medical imaging is the lack of comprehensive datasets. Addressing this issue, our study introduces CT-RATE, the first 3D medical imaging dataset that pairs images with textual reports. CT-RATE consists of 25,692 non-contrast chest CT volumes, expanded to 50,188 through various reconstructions, from 21,304 unique patients, along with corresponding radiology text reports. Leveraging CT-RATE, we developed CT-CLIP, a CT-focused contrastive language-image pre-training framework. As a versatile, self-supervised model, CT-CLIP is designed for broad application and does not require task-specific training. Remarkably, CT-CLIP outperforms state-of-the-art, fully supervised methods in multi-abnormality detection across all key metrics, thus eliminating the need for manual annotation. We also demonstrate its utility in case retrieval, whether using imagery or textual queries, thereby advancing knowledge dissemination. The open-source release of CT-RATE and CT-CLIP marks a significant advancement in medical AI, enhancing 3D imaging analysis and fostering innovation in healthcare.

Flow matching has emerged as a compelling generative modeling approach that is widely used across domains. To generate data via a flow matching model, an ordinary differential equation (ODE) is numerically solved via forward integration of the modeled velocity field. To better capture the multi-modality that is inherent in typical velocity fields, hierarchical flow matching was recently introduced. It uses a hierarchy of ODEs that are numerically integrated when generating data. This hierarchy of ODEs captures the multi-modal velocity distribution just like vanilla flow matching is capable of modeling a multi-modal data distribution. While this hierarchy enables to model multi-modal velocity distributions, the complexity of the modeled distribution remains identical across levels of the hierarchy. In this paper, we study how to gradually adjust the complexity of the distributions across different levels of the hierarchy via mini-batch couplings. We show the benefits of mini-batch couplings in hierarchical rectified flow matching via compelling results on synthetic and imaging data. Code is available at https://riccizz.github.io/HRF_coupling.

Rapid advancements in medical image segmentation performance have been significantly driven by the development of Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs). These models follow the discriminative pixel-wise classification learning paradigm and often have limited ability to generalize across diverse medical imaging datasets. In this manuscript, we introduce Generative Medical Segmentation (GMS), a novel approach leveraging a generative model to perform image segmentation. Concretely, GMS employs a robust pre-trained vision foundation model to extract latent representations for images and corresponding ground truth masks, followed by a model that learns a mapping function from the image to the mask in the latent space. Once trained, the model generates an estimated segmentation mask using the pre-trained vision foundation model to decode the predicted latent representation back into the image space. The design of GMS leads to fewer trainable parameters in the model which reduces the risk of overfitting and enhances its generalization capability. Our experimental analysis across five public datasets in different medical imaging domains demonstrates GMS outperforms existing discriminative and generative segmentation models. Furthermore, GMS is able to generalize well across datasets from different centers within the same imaging modality. Our experiments suggest GMS offers a scalable and effective solution for medical image segmentation. GMS implementation and trained model weights are available at https://github.com/King-HAW/GMS.

Giant Star-forming Clumps (GSFCs) are areas of intensive star-formation that are commonly observed in high-redshift (z>1) galaxies but their formation and role in galaxy evolution remain unclear. High-resolution observations of low-redshift clumpy galaxy analogues are rare and restricted to a limited set of galaxies but the increasing availability of wide-field galaxy survey data makes the detection of large clumpy galaxy samples increasingly feasible. Deep Learning, and in particular CNNs, have been successfully applied to image classification tasks in astrophysical data analysis. However, one application of DL that remains relatively unexplored is that of automatically identifying and localising specific objects or features in astrophysical imaging data. In this paper we demonstrate the feasibility of using Deep learning-based object detection models to localise GSFCs in astrophysical imaging data. We apply the Faster R-CNN object detection framework (FRCNN) to identify GSFCs in low redshift (z<0.3) galaxies. Unlike other studies, we train different FRCNN models not on simulated images with known labels but on real observational data that was collected by the Sloan Digital Sky Survey Legacy Survey and labelled by volunteers from the citizen science project `Galaxy Zoo: Clump Scout'. The FRCNN model relies on a CNN component as a `backbone' feature extractor. We show that CNNs, that have been pre-trained for image classification using astrophysical images, outperform those that have been pre-trained on terrestrial images. In particular, we compare a domain-specific CNN -`Zoobot' - with a generic classification backbone and find that Zoobot achieves higher detection performance and also requires smaller training data sets to do so. Our final model is capable of producing GSFC detections with a completeness and purity of >=0.8 while only being trained on ~5,000 galaxy images.

Conformal prediction is emerging as a popular paradigm for providing rigorous uncertainty quantification in machine learning since it can be easily applied as a post-processing step to already trained models. In this paper, we extend conformal prediction to the federated learning setting. The main challenge we face is data heterogeneity across the clients - this violates the fundamental tenet of exchangeability required for conformal prediction. We propose a weaker notion of partial exchangeability, better suited to the FL setting, and use it to develop the Federated Conformal Prediction (FCP) framework. We show FCP enjoys rigorous theoretical guarantees and excellent empirical performance on several computer vision and medical imaging datasets. Our results demonstrate a practical approach to incorporating meaningful uncertainty quantification in distributed and heterogeneous environments. We provide code used in our experiments https://github.com/clu5/federated-conformal.

While leveraging additional training data is well established to improve adversarial robustness, it incurs the unavoidable cost of data collection and the heavy computation to train models. To mitigate the costs, we propose Guided Adversarial Training (GAT), a novel adversarial training technique that exploits auxiliary tasks under a limited set of training data. Our approach extends single-task models into multi-task models during the min-max optimization of adversarial training, and drives the loss optimization with a regularization of the gradient curvature across multiple tasks. GAT leverages two types of auxiliary tasks: self-supervised tasks, where the labels are generated automatically, and domain-knowledge tasks, where human experts provide additional labels. Experimentally, GAT increases the robust AUC of CheXpert medical imaging dataset from 50% to 83% and On CIFAR-10, GAT outperforms eight state-of-the-art adversarial training and achieves 56.21% robust accuracy with Resnet-50. Overall, we demonstrate that guided multi-task learning is an actionable and promising avenue to push further the boundaries of model robustness.

The success of Deep Neural Network (DNN) models significantly depends on the quality of provided annotations. In medical image segmentation, for example, having multiple expert annotations for each data point is common to minimize subjective annotation bias. Then, the goal of estimation is to filter out the label noise and recover the ground-truth masks, which are not explicitly given. This paper proposes a probabilistic model for noisy observations that allows us to build a confident classification and segmentation models. To accomplish it, we explicitly model label noise and introduce a new information-based regularization that pushes the network to recover the ground-truth labels. In addition, for segmentation task we adjust the loss function by prioritizing learning in high-confidence regions where all the annotators agree on labeling. We evaluate the proposed method on a series of classification tasks such as noisy versions of MNIST, CIFAR-10, Fashion-MNIST datasets as well as CIFAR-10N, which is real-world dataset with noisy human annotations. Additionally, for segmentation task, we consider several medical imaging datasets, such as, LIDC and RIGA that reflect real-world inter-variability among multiple annotators. Our experiments show that our algorithm outperforms state-of-the-art solutions for the considered classification and segmentation problems.

We assess the dark matter halo masses of luminous AGNs over the redshift range 0.2 to 1.2 using galaxy-galaxy lensing based on imaging data from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP). We measure the weak lensing signal of a sample of 48907 AGNs constructed using HSC and WISE photometry. %The lensing detection around AGNs has a signal to noise ratio of 29. As expected, we find that the lensing mass profile of total AGN sample is consistent with that of massive galaxies (rm log(M_{*}/h^{-2}M_odot)sim 10.61). Surprisingly, the lensing signal remains unchanged when the AGN sample is split into four stellar mass bins of host galaxies. Specifically, we find that the excess surface density (ESD) of AGNs, residing in galaxies with high stellar masses, significantly differs from that of the control sample. We further fit a halo occupation distribution model to the data to infer the posterior distribution of parameters including the average halo mass. We find that the characteristic halo mass of the full AGN population lies near the knee (rm log(M_h/h^{-1}M_{odot})=12.0) of the stellar-to-halo mass relation (SHMR). Illustrative of the results given above, the halo masses of AGNs residing in host galaxies with high stellar masses (i.e., above the knee of the SHMR) falls below the calibrated SHMR while the halo mass of the low stellar mass sample is more consistent with the established SHMR. These results indicate that massive halos with higher clustering bias tends to suppress AGN activity, probably due to the lack of available gas.

Vision foundation models like DINOv2 demonstrate remarkable potential in medical imaging despite their origin in natural image domains. However, their design inherently works best for uni-modal image analysis, limiting their effectiveness for multi-modal imaging tasks that are common in many medical fields, such as neurology and oncology. While supervised models perform well in this setting, they fail to leverage unlabeled datasets and struggle with missing modalities, a frequent challenge in clinical settings. To bridge these gaps, we introduce MM-DINOv2, a novel and efficient framework that adapts the pre-trained vision foundation model DINOv2 for multi-modal medical imaging. Our approach incorporates multi-modal patch embeddings, enabling vision foundation models to effectively process multi-modal imaging data. To address missing modalities, we employ full-modality masking, which encourages the model to learn robust cross-modality relationships. Furthermore, we leverage semi-supervised learning to harness large unlabeled datasets, enhancing both the accuracy and reliability of medical predictions. Applied to glioma subtype classification from multi-sequence brain MRI, our method achieves a Matthews Correlation Coefficient (MCC) of 0.6 on an external test set, surpassing state-of-the-art supervised approaches by +11.1%. Our work establishes a scalable and robust solution for multi-modal medical imaging tasks, leveraging powerful vision foundation models pre-trained on natural images while addressing real-world clinical challenges such as missing data and limited annotations.

Transforming two-dimensional (2D) images into three-dimensional (3D) volumes is a well-known yet challenging problem for the computer vision community. In the medical domain, a few previous studies attempted to convert two or more input radiographs into computed tomography (CT) volumes. Following their effort, we introduce a diffusion model-based technology that can rotate the anatomical content of any input radiograph in 3D space, potentially enabling the visualization of the entire anatomical content of the radiograph from any viewpoint in 3D. Similar to previous studies, we used CT volumes to create Digitally Reconstructed Radiographs (DRRs) as the training data for our model. However, we addressed two significant limitations encountered in previous studies: 1. We utilized conditional diffusion models with classifier-free guidance instead of Generative Adversarial Networks (GANs) to achieve higher mode coverage and improved output image quality, with the only trade-off being slower inference time, which is often less critical in medical applications; and 2. We demonstrated that the unreliable output of style transfer deep learning (DL) models, such as Cycle-GAN, to transfer the style of actual radiographs to DRRs could be replaced with a simple yet effective training transformation that randomly changes the pixel intensity histograms of the input and ground-truth imaging data during training. This transformation makes the diffusion model agnostic to any distribution variations of the input data pixel intensity, enabling the reliable training of a DL model on input DRRs and applying the exact same model to conventional radiographs (or DRRs) during inference.

Materials characterization is fundamental to acquiring materials information, revealing the processing-microstructure-property relationships that guide material design and optimization. While multimodal large language models (MLLMs) have recently shown promise in generative and predictive tasks within materials science, their capacity to understand real-world characterization imaging data remains underexplored. To bridge this gap, we present MatCha, the first benchmark for materials characterization image understanding, comprising 1,500 questions that demand expert-level domain expertise. MatCha encompasses four key stages of materials research comprising 21 distinct tasks, each designed to reflect authentic challenges faced by materials scientists. Our evaluation of state-of-the-art MLLMs on MatCha reveals a significant performance gap compared to human experts. These models exhibit degradation when addressing questions requiring higher-level expertise and sophisticated visual perception. Simple few-shot and chain-of-thought prompting struggle to alleviate these limitations. These findings highlight that existing MLLMs still exhibit limited adaptability to real-world materials characterization scenarios. We hope MatCha will facilitate future research in areas such as new material discovery and autonomous scientific agents. MatCha is available at https://github.com/FreedomIntelligence/MatCha.

Multimodal large language models (MLLMs) have achieved significant success in the general field of image processing. Their emerging task generalization and freeform conversational capabilities can greatly facilitate medical diagnostic assistance, helping patients better understand their conditions and enhancing doctor-patient trust. Computed Tomography (CT) is a non-invasive imaging technique used to capture the internal mechanisms of a patient's condition and is widely utilized. However, in past research, the complex textural features of this imaging data have made accurate interpretation by algorithms challenging, impeding the performance of general LLMs in diagnostic assistance. To address this, we developed OrthoDoc, a MLLM designed for CT diagnostics. OrthoDoc is trained on 120,000 CT images and diagnostic reports and includes a Retrieval-Augmented Generation (RAG) module capable of effectively mitigating model hallucinations. This module is informed by extensive medical literature, textbooks, and explanatory data. Thus, OrthoDoc not only processes complex CT images but also stores, understands, and reasons over medical knowledge and language. In extensive experiments, OrthoDoc outperforms commercial models led by GPT-4, demonstrating superior diagnostic capabilities and accuracy. Specifically, OrthoDoc significantly surpasses existing models in the diagnosis of common orthopedic conditions such as fractures, arthritis, and tumors. Additionally, OrthoDoc exhibits robust generalization and stability when handling rare and complex cases.

Brain extraction and removal of skull artifacts from magnetic resonance images (MRI) is an important preprocessing step in neuroimaging analysis. There are many tools developed to handle human fMRI images, which could involve manual steps for verifying results from brain segmentation that makes it time consuming and inefficient. In this study, we will use the segment anything model (SAM), a freely available neural network released by Meta[4], which has shown promising results in many generic segmentation applications. We will analyze the efficiency of SAM for neuroimaging brain segmentation by removing skull artifacts. The results of the experiments showed promising results that explore using automated segmentation algorithms for neuroimaging without the need to train on custom medical imaging dataset.

The deep learning field is converging towards the use of general foundation models that can be easily adapted for diverse tasks. While this paradigm shift has become common practice within the field of natural language processing, progress has been slower in computer vision. In this paper we attempt to address this issue by investigating the transferability of various state-of-the-art foundation models to medical image classification tasks. Specifically, we evaluate the performance of five foundation models, namely SAM, SEEM, DINOv2, BLIP, and OpenCLIP across four well-established medical imaging datasets. We explore different training settings to fully harness the potential of these models. Our study shows mixed results. DINOv2 consistently outperforms the standard practice of ImageNet pretraining. However, other foundation models failed to consistently beat this established baseline indicating limitations in their transferability to medical image classification tasks.

Medical Vision-Language Models (MVLMs) have achieved par excellence generalization in medical image analysis, yet their performance under noisy, corrupted conditions remains largely untested. Clinical imaging is inherently susceptible to acquisition artifacts and noise; however, existing evaluations predominantly assess generally clean datasets, overlooking robustness -- i.e., the model's ability to perform under real-world distortions. To address this gap, we first introduce MediMeta-C, a corruption benchmark that systematically applies several perturbations across multiple medical imaging datasets. Combined with MedMNIST-C, this establishes a comprehensive robustness evaluation framework for MVLMs. We further propose RobustMedCLIP, a visual encoder adaptation of a pretrained MVLM that incorporates few-shot tuning to enhance resilience against corruptions. Through extensive experiments, we benchmark 5 major MVLMs across 5 medical imaging modalities, revealing that existing models exhibit severe degradation under corruption and struggle with domain-modality tradeoffs. Our findings highlight the necessity of diverse training and robust adaptation strategies, demonstrating that efficient low-rank adaptation when paired with few-shot tuning, improves robustness while preserving generalization across modalities.

Learning the response of single-cells to various treatments offers great potential to enable targeted therapies. In this context, neural optimal transport (OT) has emerged as a principled methodological framework because it inherently accommodates the challenges of unpaired data induced by cell destruction during data acquisition. However, most existing OT approaches are incapable of conditioning on different treatment contexts (e.g., time, drug treatment, drug dosage, or cell type) and we still lack methods that unanimously show promising generalization performance to unseen treatments. Here, we propose the Conditional Monge Gap which learns OT maps conditionally on arbitrary covariates. We demonstrate its value in predicting single-cell perturbation responses conditional to one or multiple drugs, a drug dosage, or combinations thereof. We find that our conditional models achieve results comparable and sometimes even superior to the condition-specific state-of-the-art on scRNA-seq as well as multiplexed protein imaging data. Notably, by aggregating data across conditions we perform cross-task learning which unlocks remarkable generalization abilities to unseen drugs or drug dosages, widely outperforming other conditional models in capturing heterogeneity (i.e., higher moments) in the perturbed population. Finally, by scaling to hundreds of conditions and testing on unseen drugs, we narrow the gap between structure-based and effect-based drug representations, suggesting a promising path to the successful prediction of perturbation effects for unseen treatments.

PURPOSE: Subarachnoid hemorrhage (SAH) entails high morbidity and mortality rates. Convolutional neural networks (CNN), a form of deep learning, are capable of generating highly accurate predictions from imaging data. Our objective was to predict mortality in SAH patients by processing the initial CT scan on a CNN based algorithm. METHODS: Retrospective multicentric study of a consecutive cohort of patients with SAH between 2011-2022. Demographic, clinical and radiological variables were analyzed. Pre-processed baseline CT scan images were used as the input for training a CNN using AUCMEDI Framework. Our model's architecture leverages the DenseNet-121 structure, employing transfer learning principles. The output variable was mortality in the first three months. Performance of the model was evaluated by statistical parameters conventionally used in studies involving artificial intelligence methods. RESULTS: Images from 219 patients were processed, 175 for training and validation of the CNN and 44 for its evaluation. 52%(115/219) of patients were female, and the median age was 58(SD=13.06) years. 18.5%(39/219) were idiopathic SAH. Mortality rate was 28.5%(63/219). The model showed good accuracy at predicting mortality in SAH patients exclusively using the images of the initial CT scan (Accuracy=74%, F1=75% and AUC=82%). CONCLUSION: Modern image processing techniques based on AI and CNN make possible to predict mortality in SAH patients with high accuracy using CT scan images as the only input. These models might be optimized by including more data and patients resulting in better training, development and performance on tasks which are beyond the skills of conventional clinical knowledge.

Foundation vision-language models are currently transforming computer vision, and are on the rise in medical imaging fueled by their very promising generalization capabilities. However, the initial attempts to transfer this new paradigm to medical imaging have shown less impressive performances than those observed in other domains, due to the significant domain shift and the complex, expert domain knowledge inherent to medical-imaging tasks. Motivated by the need for domain-expert foundation models, we present FLAIR, a pre-trained vision-language model for universal retinal fundus image understanding. To this end, we compiled 37 open-access, mostly categorical fundus imaging datasets from various sources, with up to 97 different target conditions and 284,660 images. We integrate the expert's domain knowledge in the form of descriptive textual prompts, during both pre-training and zero-shot inference, enhancing the less-informative categorical supervision of the data. Such a textual expert's knowledge, which we compiled from the relevant clinical literature and community standards, describes the fine-grained features of the pathologies as well as the hierarchies and dependencies between them. We report comprehensive evaluations, which illustrate the benefit of integrating expert knowledge and the strong generalization capabilities of FLAIR under difficult scenarios with domain shifts or unseen categories. When adapted with a lightweight linear probe, FLAIR outperforms fully-trained, dataset-focused models, more so in the few-shot regimes. Interestingly, FLAIR outperforms by a large margin more generalist, larger-scale image-language models, which emphasizes the potential of embedding experts' domain knowledge and the limitations of generalist models in medical imaging.

Detecting out-of-distribution (OOD) samples in medical imaging plays an important role for downstream medical diagnosis. However, existing OOD detectors are demonstrated on natural images composed of inter-classes and have difficulty generalizing to medical images. The key issue is the granularity of OOD data in the medical domain, where intra-class OOD samples are predominant. We focus on the generalizability of OOD detection for medical images and propose a self-supervised Cascade Variational autoencoder-based Anomaly Detector (CVAD). We use a variational autoencoders' cascade architecture, which combines latent representation at multiple scales, before being fed to a discriminator to distinguish the OOD data from the in-distribution (ID) data. Finally, both the reconstruction error and the OOD probability predicted by the binary discriminator are used to determine the anomalies. We compare the performance with the state-of-the-art deep learning models to demonstrate our model's efficacy on various open-access medical imaging datasets for both intra- and inter-class OOD. Further extensive results on datasets including common natural datasets show our model's effectiveness and generalizability. The code is available at https://github.com/XiaoyuanGuo/CVAD.

This article addresses the challenge of modeling the amplitude of spatially indexed low frequency fluctuations (ALFF) in resting state functional MRI as a function of cortical structural features and a multi-task coactivation network in the Adolescent Brain Cognitive Development (ABCD) Study. It proposes a generative model that integrates effects of spatially-varying inputs and a network-valued input using deep neural networks to capture complex non-linear and spatial associations with the output. The method models spatial smoothness, accounts for subject heterogeneity and complex associations between network and spatial images at different scales, enables accurate inference of each images effect on the output image, and allows prediction with uncertainty quantification via Monte Carlo dropout, contributing to one of the first Explainable AI (XAI) frameworks for heterogeneous imaging data. The model is highly scalable to high-resolution data without the heavy pre-processing or summarization often required by Bayesian methods. Empirical results demonstrate its strong performance compared to existing statistical and deep learning methods. We applied the XAI model to the ABCD data which revealed associations between cortical features and ALFF throughout the entire brain. Our model performed comparably to existing methods in predictive accuracy but provided superior uncertainty quantification and faster computation, demonstrating its effectiveness for large-scale neuroimaging analysis. Open-source software in Python for XAI is available.

Integrating RGB and NIR stereo imaging provides complementary spectral information, potentially enhancing robotic 3D vision in challenging lighting conditions. However, existing datasets and imaging systems lack pixel-level alignment between RGB and NIR images, posing challenges for downstream vision tasks. In this paper, we introduce a robotic vision system equipped with pixel-aligned RGB-NIR stereo cameras and a LiDAR sensor mounted on a mobile robot. The system simultaneously captures pixel-aligned pairs of RGB stereo images, NIR stereo images, and temporally synchronized LiDAR points. Utilizing the mobility of the robot, we present a dataset containing continuous video frames under diverse lighting conditions. We then introduce two methods that utilize the pixel-aligned RGB-NIR images: an RGB-NIR image fusion method and a feature fusion method. The first approach enables existing RGB-pretrained vision models to directly utilize RGB-NIR information without fine-tuning. The second approach fine-tunes existing vision models to more effectively utilize RGB-NIR information. Experimental results demonstrate the effectiveness of using pixel-aligned RGB-NIR images across diverse lighting conditions.

Reconstructing 3D visuals from functional Magnetic Resonance Imaging (fMRI) data, introduced as Recon3DMind in our conference work, is of significant interest to both cognitive neuroscience and computer vision. To advance this task, we present the fMRI-3D dataset, which includes data from 15 participants and showcases a total of 4768 3D objects. The dataset comprises two components: fMRI-Shape, previously introduced and accessible at https://huggingface.co/datasets/Fudan-fMRI/fMRI-Shape, and fMRI-Objaverse, proposed in this paper and available at https://huggingface.co/datasets/Fudan-fMRI/fMRI-Objaverse. fMRI-Objaverse includes data from 5 subjects, 4 of whom are also part of the Core set in fMRI-Shape, with each subject viewing 3142 3D objects across 117 categories, all accompanied by text captions. This significantly enhances the diversity and potential applications of the dataset. Additionally, we propose MinD-3D, a novel framework designed to decode 3D visual information from fMRI signals. The framework first extracts and aggregates features from fMRI data using a neuro-fusion encoder, then employs a feature-bridge diffusion model to generate visual features, and finally reconstructs the 3D object using a generative transformer decoder. We establish new benchmarks by designing metrics at both semantic and structural levels to evaluate model performance. Furthermore, we assess our model's effectiveness in an Out-of-Distribution setting and analyze the attribution of the extracted features and the visual ROIs in fMRI signals. Our experiments demonstrate that MinD-3D not only reconstructs 3D objects with high semantic and spatial accuracy but also deepens our understanding of how human brain processes 3D visual information. Project page at: https://jianxgao.github.io/MinD-3D.

We describe a Magnetic Resonance Imaging (MRI) dataset from individuals from the African nation of Nigeria. The dataset contains pseudonymized structural MRI (T1w, T2w, FLAIR) data of clinical quality. The dataset contains data from 36 images from healthy control subjects, 32 images from individuals diagnosed with age-related dementia and 20 from individuals with Parkinson's disease. There is currently a paucity of data from the African continent. Given the potential for Africa to contribute to the global neuroscience community, this first MRI dataset represents both an opportunity and benchmark for future studies to share data from the African continent.

In this paper, we propose a machine learning-based method for automatically classifying honey botanical origins. Dataset preparation, feature extraction, and classification are the three main steps of the proposed method. We use a class transformation method in the dataset preparation phase to maximize the separability across classes. The feature extraction phase employs the Linear Discriminant Analysis (LDA) technique for extracting relevant features and reducing the number of dimensions. In the classification phase, we use Support Vector Machines (SVM) and K-Nearest Neighbors (KNN) models to classify the extracted features of honey samples into their botanical origins. We evaluate our system using a standard honey hyperspectral imaging (HSI) dataset. Experimental findings demonstrate that the proposed system produces state-of-the-art results on this dataset, achieving the highest classification accuracy of 95.13% for hyperspectral image-based classification and 92.80% for hyperspectral instance-based classification.

This paper presents a large publicly available multi-center lumbar spine magnetic resonance imaging (MRI) dataset with reference segmentations of vertebrae, intervertebral discs (IVDs), and spinal canal. The dataset includes 447 sagittal T1 and T2 MRI series from 218 patients with a history of low back pain. It was collected from four different hospitals and was divided into a training (179 patients) and validation (39 patients) set. An iterative data annotation approach was used by training a segmentation algorithm on a small part of the dataset, enabling semi-automatic segmentation of the remaining images. The algorithm provided an initial segmentation, which was subsequently reviewed, manually corrected, and added to the training data. We provide reference performance values for this baseline algorithm and nnU-Net, which performed comparably. We set up a continuous segmentation challenge to allow for a fair comparison of different segmentation algorithms. This study may encourage wider collaboration in the field of spine segmentation, and improve the diagnostic value of lumbar spine MRI.

Deep neural networks trained on Functional Connectivity (FC) networks extracted from functional Magnetic Resonance Imaging (fMRI) data have gained popularity due to the increasing availability of data and advances in model architectures, including Graph Neural Network (GNN). Recent research on the application of GNN to FC suggests that exploiting the time-varying properties of the FC could significantly improve the accuracy and interpretability of the model prediction. However, the high cost of acquiring high-quality fMRI data and corresponding phenotypic labels poses a hurdle to their application in real-world settings, such that a model na\"ively trained in a supervised fashion can suffer from insufficient performance or a lack of generalization on a small number of data. In addition, most Self-Supervised Learning (SSL) approaches for GNNs to date adopt a contrastive strategy, which tends to lose appropriate semantic information when the graph structure is perturbed or does not leverage both spatial and temporal information simultaneously. In light of these challenges, we propose a generative SSL approach that is tailored to effectively harness spatio-temporal information within dynamic FC. Our empirical results, experimented with large-scale (>50,000) fMRI datasets, demonstrate that our approach learns valuable representations and enables the construction of accurate and robust models when fine-tuned for downstream tasks.

Reconstruction of magnetic resonance imaging (MRI) data has been positively affected by deep learning. A key challenge remains: to improve generalisation to distribution shifts between the training and testing data. Most approaches aim to address this via inductive design or data augmentation. However, they can be affected by misleading data, e.g. random noise, and cases where the inference stage data do not match assumptions in the modelled shifts. In this work, by employing a conditional hyperparameter network, we eliminate the need of augmentation, yet maintain robust performance under various levels of Gaussian noise. We demonstrate that our model withstands various input noise levels while producing high-definition reconstructions during the test stage. Moreover, we present a hyperparameter sampling strategy that accelerates the convergence of training. Our proposed method achieves the highest accuracy and image quality in all settings compared to baseline methods.

The successes of foundation models such as ChatGPT and AlphaFold have spurred significant interest in building similar models for electronic medical records (EMRs) to improve patient care and hospital operations. However, recent hype has obscured critical gaps in our understanding of these models' capabilities. We review over 80 foundation models trained on non-imaging EMR data (i.e. clinical text and/or structured data) and create a taxonomy delineating their architectures, training data, and potential use cases. We find that most models are trained on small, narrowly-scoped clinical datasets (e.g. MIMIC-III) or broad, public biomedical corpora (e.g. PubMed) and are evaluated on tasks that do not provide meaningful insights on their usefulness to health systems. In light of these findings, we propose an improved evaluation framework for measuring the benefits of clinical foundation models that is more closely grounded to metrics that matter in healthcare.

The removal of non-brain signal from magnetic resonance imaging (MRI) data, known as skull-stripping, is an integral component of many neuroimage analysis streams. Despite their abundance, popular classical skull-stripping methods are usually tailored to images with specific acquisition properties, namely near-isotropic resolution and T1-weighted (T1w) MRI contrast, which are prevalent in research settings. As a result, existing tools tend to adapt poorly to other image types, such as stacks of thick slices acquired with fast spin-echo (FSE) MRI that are common in the clinic. While learning-based approaches for brain extraction have gained traction in recent years, these methods face a similar burden, as they are only effective for image types seen during the training procedure. To achieve robust skull-stripping across a landscape of imaging protocols, we introduce SynthStrip, a rapid, learning-based brain-extraction tool. By leveraging anatomical segmentations to generate an entirely synthetic training dataset with anatomies, intensity distributions, and artifacts that far exceed the realistic range of medical images, SynthStrip learns to successfully generalize to a variety of real acquired brain images, removing the need for training data with target contrasts. We demonstrate the efficacy of SynthStrip for a diverse set of image acquisitions and resolutions across subject populations, ranging from newborn to adult. We show substantial improvements in accuracy over popular skull-stripping baselines -- all with a single trained model. Our method and labeled evaluation data are available at https://w3id.org/synthstrip.

A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark. The code is made public at https://github.com/krishnabits001/domain_specific_cl.

Brain signal visualization has emerged as an active research area, serving as a critical interface between the human visual system and computer vision models. Although diffusion models have shown promise in analyzing functional magnetic resonance imaging (fMRI) data, including reconstructing high-quality images consistent with original visual stimuli, their accuracy in extracting semantic and silhouette information from brain signals remains limited. In this regard, we propose a novel approach, referred to as Controllable Mind Visual Diffusion Model (CMVDM). CMVDM extracts semantic and silhouette information from fMRI data using attribute alignment and assistant networks. Additionally, a residual block is incorporated to capture information beyond semantic and silhouette features. We then leverage a control model to fully exploit the extracted information for image synthesis, resulting in generated images that closely resemble the visual stimuli in terms of semantics and silhouette. Through extensive experimentation, we demonstrate that CMVDM outperforms existing state-of-the-art methods both qualitatively and quantitatively.

Developing advanced medical imaging retrieval systems is challenging due to the varying definitions of `similar images' across different medical contexts. This challenge is compounded by the lack of large-scale, high-quality medical imaging retrieval datasets and benchmarks. In this paper, we propose a novel methodology that leverages dense radiology reports to define image-wise similarity ordering at multiple granularities in a scalable and fully automatic manner. Using this approach, we construct two comprehensive medical imaging retrieval datasets: MIMIC-IR for Chest X-rays and CTRATE-IR for CT scans, providing detailed image-image ranking annotations conditioned on diverse anatomical structures. Furthermore, we develop two retrieval systems, RadIR-CXR and model-ChestCT, which demonstrate superior performance in traditional image-image and image-report retrieval tasks. These systems also enable flexible, effective image retrieval conditioned on specific anatomical structures described in text, achieving state-of-the-art results on 77 out of 78 metrics.

Various tasks in data science are modeled utilizing the variational regularization approach, where manually selecting regularization parameters presents a challenge. The difficulty gets exacerbated when employing regularizers involving a large number of hyperparameters. To overcome this challenge, bilevel learning can be employed to learn such parameters from data. However, neither exact function values nor exact gradients with respect to the hyperparameters are attainable, necessitating methods that only rely on inexact evaluation of such quantities. State-of-the-art inexact gradient-based methods a priori select a sequence of the required accuracies and cannot identify an appropriate step size since the Lipschitz constant of the hypergradient is unknown. In this work, we propose an algorithm with backtracking line search that only relies on inexact function evaluations and hypergradients and show convergence to a stationary point. Furthermore, the proposed algorithm determines the required accuracy dynamically rather than manually selected before running it. Our numerical experiments demonstrate the efficiency and feasibility of our approach for hyperparameter estimation on a range of relevant problems in imaging and data science such as total variation and field of experts denoising and multinomial logistic regression. Particularly, the results show that the algorithm is robust to its own hyperparameters such as the initial accuracies and step size.

MRI super-resolution (SR) and denoising tasks are fundamental challenges in the field of deep learning, which have traditionally been treated as distinct tasks with separate paired training data. In this paper, we propose an innovative method that addresses both tasks simultaneously using a single deep learning model, eliminating the need for explicitly paired noisy and clean images during training. Our proposed model is primarily trained for SR, but also exhibits remarkable noise-cleaning capabilities in the super-resolved images. Instead of conventional approaches that introduce frequency-related operations into the generative process, our novel approach involves the use of a GAN model guided by a frequency-informed discriminator. To achieve this, we harness the power of the 3D Discrete Wavelet Transform (DWT) operation as a frequency constraint within the GAN framework for the SR task on magnetic resonance imaging (MRI) data. Specifically, our contributions include: 1) a 3D generator based on residual-in-residual connected blocks; 2) the integration of the 3D DWT with 1times 1 convolution into a DWT+conv unit within a 3D Unet for the discriminator; 3) the use of the trained model for high-quality image SR, accompanied by an intrinsic denoising process. We dub the model "Denoising Induced Super-resolution GAN (DISGAN)" due to its dual effects of SR image generation and simultaneous denoising. Departing from the traditional approach of training SR and denoising tasks as separate models, our proposed DISGAN is trained only on the SR task, but also achieves exceptional performance in denoising. The model is trained on 3D MRI data from dozens of subjects from the Human Connectome Project (HCP) and further evaluated on previously unseen MRI data from subjects with brain tumours and epilepsy to assess its denoising and SR performance.

Deep learning in medical imaging has the potential to minimize the risk of diagnostic errors, reduce radiologist workload, and accelerate diagnosis. Training such deep learning models requires large and accurate datasets, with annotations for all training samples. However, in the medical imaging domain, annotated datasets for specific tasks are often small due to the high complexity of annotations, limited access, or the rarity of diseases. To address this challenge, deep learning models can be pre-trained on large image datasets without annotations using methods from the field of self-supervised learning. After pre-training, small annotated datasets are sufficient to fine-tune the models for a specific task. The most popular self-supervised pre-training approaches in medical imaging are based on contrastive learning. However, recent studies in natural image processing indicate a strong potential for masked autoencoder approaches. Our work compares state-of-the-art contrastive learning methods with the recently introduced masked autoencoder approach "SparK" for convolutional neural networks (CNNs) on medical images. Therefore we pre-train on a large unannotated CT image dataset and fine-tune on several CT classification tasks. Due to the challenge of obtaining sufficient annotated training data in medical imaging, it is of particular interest to evaluate how the self-supervised pre-training methods perform when fine-tuning on small datasets. By experimenting with gradually reducing the training dataset size for fine-tuning, we find that the reduction has different effects depending on the type of pre-training chosen. The SparK pre-training method is more robust to the training dataset size than the contrastive methods. Based on our results, we propose the SparK pre-training for medical imaging tasks with only small annotated datasets.

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

Deep learning has demonstrated remarkable success in medical image segmentation and computer-aided diagnosis. In particular, numerous advanced methods have achieved state-of-the-art performance in brain tumor segmentation from MRI scans. While recent studies in other medical imaging domains have revealed that integrating textual reports with visual data can enhance segmentation accuracy, the field of brain tumor analysis lacks a comprehensive dataset that combines radiological images with corresponding textual annotations. This limitation has hindered the exploration of multimodal approaches that leverage both imaging and textual data. To bridge this critical gap, we introduce the TextBraTS dataset, the first publicly available volume-level multimodal dataset that contains paired MRI volumes and rich textual annotations, derived from the widely adopted BraTS2020 benchmark. Building upon this novel dataset, we propose a novel baseline framework and sequential cross-attention method for text-guided volumetric medical image segmentation. Through extensive experiments with various text-image fusion strategies and templated text formulations, our approach demonstrates significant improvements in brain tumor segmentation accuracy, offering valuable insights into effective multimodal integration techniques. Our dataset, implementation code, and pre-trained models are publicly available at https://github.com/Jupitern52/TextBraTS.

Self-supervised learning has emerged as a powerful paradigm for training deep neural networks, particularly in medical imaging where labeled data is scarce. While current approaches typically rely on synthetic augmentations of single images, we propose VET-DINO, a framework that leverages a unique characteristic of medical imaging: the availability of multiple standardized views from the same study. Using a series of clinical veterinary radiographs from the same patient study, we enable models to learn view-invariant anatomical structures and develop an implied 3D understanding from 2D projections. We demonstrate our approach on a dataset of 5 million veterinary radiographs from 668,000 canine studies. Through extensive experimentation, including view synthesis and downstream task performance, we show that learning from real multi-view pairs leads to superior anatomical understanding compared to purely synthetic augmentations. VET-DINO achieves state-of-the-art performance on various veterinary imaging tasks. Our work establishes a new paradigm for self-supervised learning in medical imaging that leverages domain-specific properties rather than merely adapting natural image techniques.

Purpose: Hard-to-interpret Black-box Machine Learning (ML) were often used for early Alzheimer's Disease (AD) detection. Methods: To interpret eXtreme Gradient Boosting (XGBoost), Random Forest (RF), and Support Vector Machine (SVM) black-box models a workflow based on Shapley values was developed. All models were trained on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset and evaluated for an independent ADNI test set, as well as the external Australian Imaging and Lifestyle flagship study of Ageing (AIBL), and Open Access Series of Imaging Studies (OASIS) datasets. Shapley values were compared to intuitively interpretable Decision Trees (DTs), and Logistic Regression (LR), as well as natural and permutation feature importances. To avoid the reduction of the explanation validity caused by correlated features, forward selection and aspect consolidation were implemented. Results: Some black-box models outperformed DTs and LR. The forward-selected features correspond to brain areas previously associated with AD. Shapley values identified biologically plausible associations with moderate to strong correlations with feature importances. The most important RF features to predict AD conversion were the volume of the amygdalae, and a cognitive test score. Good cognitive test performances and large brain volumes decreased the AD risk. The models trained using cognitive test scores significantly outperformed brain volumetric models (p<0.05). Cognitive Normal (CN) vs. AD models were successfully transferred to external datasets. Conclusion: In comparison to previous work, improved performances for ADNI and AIBL were achieved for CN vs. Mild Cognitive Impairment (MCI) classification using brain volumes. The Shapley values and the feature importances showed moderate to strong correlations.

This study explores cardiovascular stents fabricated using laser powder bed fusion (LPBF); an emerging method to offer patient-specific customisable parts. Here, the shape memory alloy NiTi, in a near equiatomic composition, was investigated to deconvolve the material response from macroscopic component effects. Specifically, stress-geometry interactions were revealed, in-situ, for a minaturised cardiovascular stent subjected to an externally applied cylindrical stress whilst acquiring synchrotron X-ray imaging and diffraction data. The approach enabled the collection of spatially resolved micromechanical deformation data; the formation of stress-induced martensite and R-phase was evident, occurring in locations near junctions between stent ligaments where stress concentrations exist. In the as-fabricated condition, hardness maps were obtained through nanoindentation, demonstrating that the localised deformation and deformation patterning is further controlled by porosity and microstructural heterogeneity. Electron backscatter diffraction (EBSD) supported these observations, showing a finer grain structure near stent junctions with higher associated lattice curvature. These features, combined with stress concentrations when loaded will initiate localised phase transformations. If the stent was subjected to repeated loading, representing in-vivo conditions, these regions would be susceptible to cyclic damage through transformation memory loss, leading to premature component failure. This study highlights the challenges that must be addressed for the post-processing treatment of LABF-processed stents for healthcare-related applications.

Classical self-supervised networks suffer from convergence problems and reduced segmentation accuracy due to forceful termination. Qubits or bi-level quantum bits often describe quantum neural network models. In this article, a novel self-supervised shallow learning network model exploiting the sophisticated three-level qutrit-inspired quantum information system referred to as Quantum Fully Self-Supervised Neural Network (QFS-Net) is presented for automated segmentation of brain MR images. The QFS-Net model comprises a trinity of a layered structure of qutrits inter-connected through parametric Hadamard gates using an 8-connected second-order neighborhood-based topology. The non-linear transformation of the qutrit states allows the underlying quantum neural network model to encode the quantum states, thereby enabling a faster self-organized counter-propagation of these states between the layers without supervision. The suggested QFS-Net model is tailored and extensively validated on Cancer Imaging Archive (TCIA) data set collected from Nature repository and also compared with state of the art supervised (U-Net and URes-Net architectures) and the self-supervised QIS-Net model. Results shed promising segmented outcome in detecting tumors in terms of dice similarity and accuracy with minimum human intervention and computational resources.

Natural Language Generation (NLG) accepts input data in the form of images, videos, or text and generates corresponding natural language text as output. Existing NLG methods mainly adopt a supervised approach and rely heavily on coupled data-to-text pairs. However, for many targeted scenarios and for non-English languages, sufficient quantities of labeled data are often not available. To relax the dependency on labeled data of downstream tasks, we propose an intuitive and effective zero-shot learning framework, ZeroNLG, which can deal with multiple NLG tasks, including image-to-text (image captioning), video-to-text (video captioning), and text-to-text (neural machine translation), across English, Chinese, German, and French within a unified framework. ZeroNLG does not require any labeled downstream pairs for training. During training, ZeroNLG (i) projects different domains (across modalities and languages) to corresponding coordinates in a shared common latent space; (ii) bridges different domains by aligning their corresponding coordinates in this space; and (iii) builds an unsupervised multilingual auto-encoder to learn to generate text by reconstructing the input text given its coordinate in shared latent space. Consequently, during inference, based on the data-to-text pipeline, ZeroNLG can generate target sentences across different languages given the coordinate of input data in the common space. Within this unified framework, given visual (imaging or video) data as input, ZeroNLG can perform zero-shot visual captioning; given textual sentences as input, ZeroNLG can perform zero-shot machine translation. We present the results of extensive experiments on twelve NLG tasks, showing that, without using any labeled downstream pairs for training, ZeroNLG generates high-quality and believable outputs and significantly outperforms existing zero-shot methods.

LSST and Euclid must address the daunting challenge of analyzing the unprecedented volumes of imaging and spectroscopic data that these next-generation instruments will generate. A promising approach to overcoming this challenge involves rapid, automatic image processing using appropriately trained Deep Learning (DL) algorithms. However, reliable application of DL requires large, accurately labeled samples of training data. Galaxy Zoo Express (GZX) is a recent experiment that simulated using Bayesian inference to dynamically aggregate binary responses provided by citizen scientists via the Zooniverse crowd-sourcing platform in real time. The GZX approach enables collaboration between human and machine classifiers and provides rapidly generated, reliably labeled datasets, thereby enabling online training of accurate machine classifiers. We present selected results from GZX and show how the Bayesian aggregation engine it uses can be extended to efficiently provide object-localization and bounding-box annotations of two-dimensional data with quantified reliability. DL algorithms that are trained using these annotations will facilitate numerous panchromatic data modeling tasks including morphological classification and substructure detection in direct imaging, as well as decontamination and emission line identification for slitless spectroscopy. Effectively combining the speed of modern computational analyses with the human capacity to extrapolate from few examples will be critical if the potential of forthcoming large-scale surveys is to be realized.

We introduce a Three-Dimensional Convolutional Variational Autoencoder (3D-CVAE) for automated anomaly detection in Electron Energy Loss Spectroscopy Spectrum Imaging (EELS-SI) data. Our approach leverages the full three-dimensional structure of EELS-SI data to detect subtle spectral anomalies while preserving both spatial and spectral correlations across the datacube. By employing negative log-likelihood loss and training on bulk spectra, the model learns to reconstruct bulk features characteristic of the defect-free material. In exploring methods for anomaly detection, we evaluated both our 3D-CVAE approach and Principal Component Analysis (PCA), testing their performance using Fe L-edge peak shifts designed to simulate material defects. Our results show that 3D-CVAE achieves superior anomaly detection and maintains consistent performance across various shift magnitudes. The method demonstrates clear bimodal separation between normal and anomalous spectra, enabling reliable classification. Further analysis verifies that lower dimensional representations are robust to anomalies in the data. While performance advantages over PCA diminish with decreasing anomaly concentration, our method maintains high reconstruction quality even in challenging, noise-dominated spectral regions. This approach provides a robust framework for unsupervised automated detection of spectral anomalies in EELS-SI data, particularly valuable for analyzing complex material systems.

Label noise is prevalent in machine learning datasets. It is crucial to identify and remove label noise because models trained on noisy data can have substantially reduced accuracy and generalizability. Most existing label noise detection approaches are designed for classification tasks, and data cleaning for outcome prediction analysis is relatively unexplored. Inspired by the fluctuations in performance across different folds in cross-validation, we propose Repeated Cross-Validations for label noise estimation (ReCoV) to address this gap. ReCoV constructs a noise histogram that ranks the noise level of samples based on a large number of cross-validations by recording sample IDs in each worst-performing fold. We further propose three approaches for identifying noisy samples based on noise histograms to address increasingly complex noise distributions. We show that ReCoV outperforms state-of-the-art algorithms for label cleaning in a classification task benchmark. More importantly, we show that removing ReCoV-identified noisy samples in two medical imaging outcome prediction datasets significantly improves model performance on test sets. As a statistical approach that does not rely on hyperparameters, noise distributions, or model structures, ReCoV is compatible with any machine learning analysis.

Radiology reports are one of the main forms of communication between radiologists and other clinicians and contain important information for patient care. In order to use this information for research and automated patient care programs, it is necessary to convert the raw text into structured data suitable for analysis. State-of-the-art natural language processing (NLP) domain-specific contextual word embeddings have been shown to achieve impressive accuracy for these tasks in medicine, but have yet to be utilized for section structure segmentation. In this work, we pre-trained a contextual embedding BERT model using breast radiology reports and developed a classifier that incorporated the embedding with auxiliary global textual features in order to perform section segmentation. This model achieved a 98% accuracy at segregating free text reports sentence by sentence into sections of information outlined in the Breast Imaging Reporting and Data System (BI-RADS) lexicon, a significant improvement over the Classic BERT model without auxiliary information. We then evaluated whether using section segmentation improved the downstream extraction of clinically relevant information such as modality/procedure, previous cancer, menopausal status, the purpose of the exam, breast density, and breast MRI background parenchymal enhancement. Using the BERT model pre-trained on breast radiology reports combined with section segmentation resulted in an overall accuracy of 95.9% in the field extraction tasks. This is a 17% improvement compared to an overall accuracy of 78.9% for field extraction with models using Classic BERT embeddings and not using section segmentation. Our work shows the strength of using BERT in radiology report analysis and the advantages of section segmentation in identifying key features of patient factors recorded in breast radiology reports.

Accurately predicting immunotherapy response in Non-Small Cell Lung Cancer (NSCLC) remains a critical unmet need. Existing radiomics and deep learning-based predictive models rely primarily on pre-treatment imaging to predict categorical response outcomes, limiting their ability to capture the complex morphological and textural transformations induced by immunotherapy. This study introduces ImmunoDiff, an anatomy-aware diffusion model designed to synthesize post-treatment CT scans from baseline imaging while incorporating clinically relevant constraints. The proposed framework integrates anatomical priors, specifically lobar and vascular structures, to enhance fidelity in CT synthesis. Additionally, we introduce a novel cbi-Adapter, a conditioning module that ensures pairwise-consistent multimodal integration of imaging and clinical data embeddings, to refine the generative process. Additionally, a clinical variable conditioning mechanism is introduced, leveraging demographic data, blood-based biomarkers, and PD-L1 expression to refine the generative process. Evaluations on an in-house NSCLC cohort treated with immune checkpoint inhibitors demonstrate a 21.24% improvement in balanced accuracy for response prediction and a 0.03 increase in c-index for survival prediction. Code will be released soon.

Breast density estimation is one of the key tasks in recognizing individuals predisposed to breast cancer. It is often challenging because of low contrast and fluctuations in mammograms' fatty tissue background. Most of the time, the breast density is estimated manually where a radiologist assigns one of the four density categories decided by the Breast Imaging and Reporting Data Systems (BI-RADS). There have been efforts in the direction of automating a breast density classification pipeline. Breast density estimation is one of the key tasks performed during a screening exam. Dense breasts are more susceptible to breast cancer. The density estimation is challenging because of low contrast and fluctuations in mammograms' fatty tissue background. Traditional mammograms are being replaced by tomosynthesis and its other low radiation dose variants (for example Hologic' Intelligent 2D and C-View). Because of the low-dose requirement, increasingly more screening centers are favoring the Intelligent 2D view and C-View. Deep-learning studies for breast density estimation use only a single modality for training a neural network. However, doing so restricts the number of images in the dataset. In this paper, we show that a neural network trained on all the modalities at once performs better than a neural network trained on any single modality. We discuss these results using the area under the receiver operator characteristics curves.

Purpose: Medical imaging has become increasingly important in diagnosing and treating oncological patients, particularly in radiotherapy. Recent advances in synthetic computed tomography (sCT) generation have increased interest in public challenges to provide data and evaluation metrics for comparing different approaches openly. This paper describes a dataset of brain and pelvis computed tomography (CT) images with rigidly registered CBCT and MRI images to facilitate the development and evaluation of sCT generation for radiotherapy planning. Acquisition and validation methods: The dataset consists of CT, CBCT, and MRI of 540 brains and 540 pelvic radiotherapy patients from three Dutch university medical centers. Subjects' ages ranged from 3 to 93 years, with a mean age of 60. Various scanner models and acquisition settings were used across patients from the three data-providing centers. Details are available in CSV files provided with the datasets. Data format and usage notes: The data is available on Zenodo (https://doi.org/10.5281/zenodo.7260705) under the SynthRAD2023 collection. The images for each subject are available in nifti format. Potential applications: This dataset will enable the evaluation and development of image synthesis algorithms for radiotherapy purposes on a realistic multi-center dataset with varying acquisition protocols. Synthetic CT generation has numerous applications in radiation therapy, including diagnosis, treatment planning, treatment monitoring, and surgical planning.

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

Medical imaging papers often focus on methodology, but the quality of the algorithms and the validity of the conclusions are highly dependent on the datasets used. As creating datasets requires a lot of effort, researchers often use publicly available datasets, there is however no adopted standard for citing the datasets used in scientific papers, leading to difficulty in tracking dataset usage. In this work, we present two open-source tools we created that could help with the detection of dataset usage, a pipeline https://github.com/TheoSourget/Public_Medical_Datasets_References using OpenAlex and full-text analysis, and a PDF annotation software https://github.com/TheoSourget/pdf_annotator used in our study to manually label the presence of datasets. We applied both tools on a study of the usage of 20 publicly available medical datasets in papers from MICCAI and MIDL. We compute the proportion and the evolution between 2013 and 2023 of 3 types of presence in a paper: cited, mentioned in the full text, cited and mentioned. Our findings demonstrate the concentration of the usage of a limited set of datasets. We also highlight different citing practices, making the automation of tracking difficult.

Magnetic resonance imaging (MRI) is a central modality for stroke imaging. It is used upon patient admission to make treatment decisions such as selecting patients for intravenous thrombolysis or endovascular therapy. MRI is later used in the duration of hospital stay to predict outcome by visualizing infarct core size and location. Furthermore, it may be used to characterize stroke etiology, e.g. differentiation between (cardio)-embolic and non-embolic stroke. Computer based automated medical image processing is increasingly finding its way into clinical routine. Previous iterations of the Ischemic Stroke Lesion Segmentation (ISLES) challenge have aided in the generation of identifying benchmark methods for acute and sub-acute ischemic stroke lesion segmentation. Here we introduce an expert-annotated, multicenter MRI dataset for segmentation of acute to subacute stroke lesions. This dataset comprises 400 multi-vendor MRI cases with high variability in stroke lesion size, quantity and location. It is split into a training dataset of n=250 and a test dataset of n=150. All training data will be made publicly available. The test dataset will be used for model validation only and will not be released to the public. This dataset serves as the foundation of the ISLES 2022 challenge with the goal of finding algorithmic methods to enable the development and benchmarking of robust and accurate segmentation algorithms for ischemic stroke.

Segment Anything Model (SAM) has achieved impressive results for natural image segmentation with input prompts such as points and bounding boxes. Its success largely owes to massive labeled training data. However, directly applying SAM to medical image segmentation cannot perform well because SAM lacks medical knowledge -- it does not use medical images for training. To incorporate medical knowledge into SAM, we introduce SA-Med2D-20M, a large-scale segmentation dataset of 2D medical images built upon numerous public and private datasets. It consists of 4.6 million 2D medical images and 19.7 million corresponding masks, covering almost the whole body and showing significant diversity. This paper describes all the datasets collected in SA-Med2D-20M and details how to process these datasets. Furthermore, comprehensive statistics of SA-Med2D-20M are presented to facilitate the better use of our dataset, which can help the researchers build medical vision foundation models or apply their models to downstream medical applications. We hope that the large scale and diversity of SA-Med2D-20M can be leveraged to develop medical artificial intelligence for enhancing diagnosis, medical image analysis, knowledge sharing, and education. The data with the redistribution license is publicly available at https://github.com/OpenGVLab/SAM-Med2D.

Chest X-rays (CXR) are the most common medical imaging study and are used to diagnose multiple medical conditions. This study examines the impact of synthetic data supplementation, using diffusion models, on the performance of deep learning (DL) classifiers for CXR analysis. We employed three datasets: CheXpert, MIMIC-CXR, and Emory Chest X-ray, training conditional denoising diffusion probabilistic models (DDPMs) to generate synthetic frontal radiographs. Our approach ensured that synthetic images mirrored the demographic and pathological traits of the original data. Evaluating the classifiers' performance on internal and external datasets revealed that synthetic data supplementation enhances model accuracy, particularly in detecting less prevalent pathologies. Furthermore, models trained on synthetic data alone approached the performance of those trained on real data. This suggests that synthetic data can potentially compensate for real data shortages in training robust DL models. However, despite promising outcomes, the superiority of real data persists.

The detection and removal of landmines is a complex and risky task that requires advanced remote sensing techniques to reduce the risk for the professionals involved in this task. In this paper, we propose a novel synthetic dataset for buried landmine detection to provide researchers with a valuable resource to observe, measure, locate, and address issues in landmine detection. The dataset consists of 41,800 microwave holographic images (2D) and their holographic inverted scans (3D) of different types of buried objects, including landmines, clutter, and pottery objects, and is collected by means of a microwave holography sensor. We evaluate the performance of several state-of-the-art deep learning models trained on our synthetic dataset for various classification tasks. While the results do not yield yet high performances, showing the difficulty of the proposed task, we believe that our dataset has significant potential to drive progress in the field of landmine detection thanks to the accuracy and resolution obtainable using holographic radars. To the best of our knowledge, our dataset is the first of its kind and will help drive further research on computer vision methods to automatize mine detection, with the overall goal of reducing the risks and the costs of the demining process.

Automated data labeling techniques are crucial for accelerating the development of deep learning models, particularly in complex medical imaging applications. However, ensuring accuracy and efficiency remains challenging. This paper presents iterative refinement strategies for automated data labeling in facial landmark diagnosis to enhance accuracy and efficiency for deep learning models in medical applications, including dermatology, plastic surgery, and ophthalmology. Leveraging feedback mechanisms and advanced algorithms, our approach iteratively refines initial labels, reducing reliance on manual intervention while improving label quality. Through empirical evaluation and case studies, we demonstrate the effectiveness of our proposed strategies in deep learning tasks across medical imaging domains. Our results highlight the importance of iterative refinement in automated data labeling to enhance the capabilities of deep learning systems in medical imaging applications.

Resection and whole brain radiotherapy (WBRT) are the standards of care for the treatment of patients with brain metastases (BM) but are often associated with cognitive side effects. Stereotactic radiosurgery (SRS) involves a more targeted treatment approach and has been shown to avoid the side effects associated with WBRT. However, SRS requires precise identification and delineation of BM. While many AI algorithms have been developed for this purpose, their clinical adoption has been limited due to poor model performance in the clinical setting. Major reasons for non-generalizable algorithms are the limitations in the datasets used for training the AI network. The purpose of this study was to create a large, heterogenous, annotated BM dataset for training and validation of AI models to improve generalizability. We present a BM dataset of 200 patients with pretreatment T1, T1 post-contrast, T2, and FLAIR MR images. The dataset includes contrast-enhancing and necrotic 3D segmentations on T1 post-contrast and whole tumor (including peritumoral edema) 3D segmentations on FLAIR. Our dataset contains 975 contrast-enhancing lesions, many of which are sub centimeter, along with clinical and imaging feature information. We used a streamlined approach to database-building leveraging a PACS-integrated segmentation workflow.

Currently, deep learning-based instance segmentation for various applications (e.g., Agriculture) is predominantly performed using a labor-intensive process involving extensive field data collection using sophisticated sensors, followed by careful manual annotation of images, presenting significant logistical and financial challenges to researchers and organizations. The process also slows down the model development and training process. In this study, we presented a novel method for deep learning-based instance segmentation of apples in commercial orchards that eliminates the need for labor-intensive field data collection and manual annotation. Utilizing a Large Language Model (LLM), we synthetically generated orchard images and automatically annotated them using the Segment Anything Model (SAM) integrated with a YOLO11 base model. This method significantly reduces reliance on physical sensors and manual data processing, presenting a major advancement in "Agricultural AI". The synthetic, auto-annotated dataset was used to train the YOLO11 model for Apple instance segmentation, which was then validated on real orchard images. The results showed that the automatically generated annotations achieved a Dice Coefficient of 0.9513 and an IoU of 0.9303, validating the accuracy and overlap of the mask annotations. All YOLO11 configurations, trained solely on these synthetic datasets with automated annotations, accurately recognized and delineated apples, highlighting the method's efficacy. Specifically, the YOLO11m-seg configuration achieved a mask precision of 0.902 and a mask mAP@50 of 0.833 on test images collected from a commercial orchard. Additionally, the YOLO11l-seg configuration outperformed other models in validation on 40 LLM-generated images, achieving the highest mask precision and mAP@50 metrics. Keywords: YOLO, SAM, SAMv2, YOLO11, YOLOv11, Segment Anything, YOLO-SAM

Purpose: Magnetic resonance imaging (MRI) to visualize anatomical motion is becoming increasingly important when treating cancer patients with radiotherapy. Hybrid MRI-linear accelerator (MRI-linac) systems allow real-time motion management during irradiation. This paper presents a multi-institutional real-time MRI time series dataset from different MRI-linac vendors. The dataset is designed to support developing and evaluating real-time tumor localization (tracking) algorithms for MRI-guided radiotherapy within the TrackRAD2025 challenge (https://trackrad2025.grand-challenge.org/). Acquisition and validation methods: The dataset consists of sagittal 2D cine MRIs in 585 patients from six centers (3 Dutch, 1 German, 1 Australian, and 1 Chinese). Tumors in the thorax, abdomen, and pelvis acquired on two commercially available MRI-linacs (0.35 T and 1.5 T) were included. For 108 cases, irradiation targets or tracking surrogates were manually segmented on each temporal frame. The dataset was randomly split into a public training set of 527 cases (477 unlabeled and 50 labeled) and a private testing set of 58 cases (all labeled). Data Format and Usage Notes: The data is publicly available under the TrackRAD2025 collection: https://doi.org/10.57967/hf/4539. Both the images and segmentations for each patient are available in metadata format. Potential Applications: This novel clinical dataset will enable the development and evaluation of real-time tumor localization algorithms for MRI-guided radiotherapy. By enabling more accurate motion management and adaptive treatment strategies, this dataset has the potential to advance the field of radiotherapy significantly.

Magnetic resonance imaging (MRI) is a cornerstone of modern medical imaging. However, long image acquisition times, the need for qualitative expert analysis, and the lack of (and difficulty extracting) quantitative indicators that are sensitive to tissue health have curtailed widespread clinical and research studies. While recent machine learning methods for MRI reconstruction and analysis have shown promise for reducing this burden, these techniques are primarily validated with imperfect image quality metrics, which are discordant with clinically-relevant measures that ultimately hamper clinical deployment and clinician trust. To mitigate this challenge, we present the Stanford Knee MRI with Multi-Task Evaluation (SKM-TEA) dataset, a collection of quantitative knee MRI (qMRI) scans that enables end-to-end, clinically-relevant evaluation of MRI reconstruction and analysis tools. This 1.6TB dataset consists of raw-data measurements of ~25,000 slices (155 patients) of anonymized patient MRI scans, the corresponding scanner-generated DICOM images, manual segmentations of four tissues, and bounding box annotations for sixteen clinically relevant pathologies. We provide a framework for using qMRI parameter maps, along with image reconstructions and dense image labels, for measuring the quality of qMRI biomarker estimates extracted from MRI reconstruction, segmentation, and detection techniques. Finally, we use this framework to benchmark state-of-the-art baselines on this dataset. We hope our SKM-TEA dataset and code can enable a broad spectrum of research for modular image reconstruction and image analysis in a clinically informed manner. Dataset access, code, and benchmarks are available at https://github.com/StanfordMIMI/skm-tea.

Medical imaging plays a crucial role in diagnosis, with radiology reports serving as vital documentation. Automating report generation has emerged as a critical need to alleviate the workload of radiologists. While machine learning has facilitated report generation for 2D medical imaging, extending this to 3D has been unexplored due to computational complexity and data scarcity. We introduce the first method to generate radiology reports for 3D medical imaging, specifically targeting chest CT volumes. Given the absence of comparable methods, we establish a baseline using an advanced 3D vision encoder in medical imaging to demonstrate our method's effectiveness, which leverages a novel auto-regressive causal transformer. Furthermore, recognizing the benefits of leveraging information from previous visits, we augment CT2Rep with a cross-attention-based multi-modal fusion module and hierarchical memory, enabling the incorporation of longitudinal multimodal data. Access our code at https://github.com/ibrahimethemhamamci/CT2Rep

The chest X-ray is one of the most commonly accessible radiological examinations for screening and diagnosis of many lung diseases. A tremendous number of X-ray imaging studies accompanied by radiological reports are accumulated and stored in many modern hospitals' Picture Archiving and Communication Systems (PACS). On the other side, it is still an open question how this type of hospital-size knowledge database containing invaluable imaging informatics (i.e., loosely labeled) can be used to facilitate the data-hungry deep learning paradigms in building truly large-scale high precision computer-aided diagnosis (CAD) systems. In this paper, we present a new chest X-ray database, namely "ChestX-ray8", which comprises 108,948 frontal-view X-ray images of 32,717 unique patients with the text-mined eight disease image labels (where each image can have multi-labels), from the associated radiological reports using natural language processing. Importantly, we demonstrate that these commonly occurring thoracic diseases can be detected and even spatially-located via a unified weakly-supervised multi-label image classification and disease localization framework, which is validated using our proposed dataset. Although the initial quantitative results are promising as reported, deep convolutional neural network based "reading chest X-rays" (i.e., recognizing and locating the common disease patterns trained with only image-level labels) remains a strenuous task for fully-automated high precision CAD systems. Data download link: https://nihcc.app.box.com/v/ChestXray-NIHCC

Chest radiography is an extremely powerful imaging modality, allowing for a detailed inspection of a patient's thorax, but requiring specialized training for proper interpretation. With the advent of high performance general purpose computer vision algorithms, the accurate automated analysis of chest radiographs is becoming increasingly of interest to researchers. However, a key challenge in the development of these techniques is the lack of sufficient data. Here we describe MIMIC-CXR-JPG v2.0.0, a large dataset of 377,110 chest x-rays associated with 227,827 imaging studies sourced from the Beth Israel Deaconess Medical Center between 2011 - 2016. Images are provided with 14 labels derived from two natural language processing tools applied to the corresponding free-text radiology reports. MIMIC-CXR-JPG is derived entirely from the MIMIC-CXR database, and aims to provide a convenient processed version of MIMIC-CXR, as well as to provide a standard reference for data splits and image labels. All images have been de-identified to protect patient privacy. The dataset is made freely available to facilitate and encourage a wide range of research in medical computer vision.

Positron emission tomography (PET) is a cornerstone of modern oncologic and neurologic imaging, distinguished by its unique ability to illuminate dynamic metabolic processes that transcend the anatomical focus of traditional imaging technologies. Radiology reports are essential for clinical decision making, yet their manual creation is labor-intensive and time-consuming. Recent advancements of vision-language models (VLMs) have shown strong potential in medical applications, presenting a promising avenue for automating report generation. However, existing applications of VLMs in the medical domain have predominantly focused on structural imaging modalities, while the unique characteristics of molecular PET imaging have largely been overlooked. To bridge the gap, we introduce PET2Rep, a large-scale comprehensive benchmark for evaluation of general and medical VLMs for radiology report generation for PET images. PET2Rep stands out as the first dedicated dataset for PET report generation with metabolic information, uniquely capturing whole-body image-report pairs that cover dozens of organs to fill the critical gap in existing benchmarks and mirror real-world clinical comprehensiveness. In addition to widely recognized natural language generation metrics, we introduce a series of clinical efficiency metrics to evaluate the quality of radiotracer uptake pattern description in key organs in generated reports. We conduct a head-to-head comparison of 30 cutting-edge general-purpose and medical-specialized VLMs. The results show that the current state-of-the-art VLMs perform poorly on PET report generation task, falling considerably short of fulfilling practical needs. Moreover, we identify several key insufficiency that need to be addressed to advance the development in medical applications.

In this work, we present MedImageInsight, an open-source medical imaging embedding model. MedImageInsight is trained on medical images with associated text and labels across a diverse collection of domains, including X-Ray, CT, MRI, dermoscopy, OCT, fundus photography, ultrasound, histopathology, and mammography. Rigorous evaluations demonstrate MedImageInsight's ability to achieve state-of-the-art (SOTA) or human expert level performance across classification, image-image search, and fine-tuning tasks. Specifically, on public datasets, MedImageInsight achieves SOTA in CT 3D medical image retrieval, as well as SOTA in disease classification and search for chest X-ray, dermatology, and OCT imaging. Furthermore, MedImageInsight achieves human expert performance in bone age estimation (on both public and partner data), as well as AUC above 0.9 in most other domains. When paired with a text decoder, MedImageInsight achieves near SOTA level single image report findings generation with less than 10\% the parameters of other models. Compared to fine-tuning GPT-4o with only MIMIC-CXR data for the same task, MedImageInsight outperforms in clinical metrics, but underperforms on lexical metrics where GPT-4o sets a new SOTA. Importantly for regulatory purposes, MedImageInsight can generate ROC curves, adjust sensitivity and specificity based on clinical need, and provide evidence-based decision support through image-image search (which can also enable retrieval augmented generation). In an independent clinical evaluation of image-image search in chest X-ray, MedImageInsight outperformed every other publicly available foundation model evaluated by large margins (over 6 points AUC), and significantly outperformed other models in terms of AI fairness (across age and gender). We hope releasing MedImageInsight will help enhance collective progress in medical imaging AI research and development.

We present a labeled large-scale, high resolution chest x-ray dataset for the automated exploration of medical images along with their associated reports. This dataset includes more than 160,000 images obtained from 67,000 patients that were interpreted and reported by radiologists at Hospital San Juan Hospital (Spain) from 2009 to 2017, covering six different position views and additional information on image acquisition and patient demography. The reports were labeled with 174 different radiographic findings, 19 differential diagnoses and 104 anatomic locations organized as a hierarchical taxonomy and mapped onto standard Unified Medical Language System (UMLS) terminology. Of these reports, 27% were manually annotated by trained physicians and the remaining set was labeled using a supervised method based on a recurrent neural network with attention mechanisms. The labels generated were then validated in an independent test set achieving a 0.93 Micro-F1 score. To the best of our knowledge, this is one of the largest public chest x-ray database suitable for training supervised models concerning radiographs, and the first to contain radiographic reports in Spanish. The PadChest dataset can be downloaded from http://bimcv.cipf.es/bimcv-projects/padchest/.

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. To exploit this structured information, we propose the use of Space-aware Memory Queues for In-painting and Detecting anomalies from radiography images (abbreviated as SQUID). We show that SQUID can taxonomize the ingrained anatomical structures into recurrent patterns; and in the inference, it can identify anomalies (unseen/modified patterns) in the image. SQUID surpasses 13 state-of-the-art methods in unsupervised anomaly detection by at least 5 points on two chest X-ray benchmark datasets measured by the Area Under the Curve (AUC). Additionally, we have created a new dataset (DigitAnatomy), which synthesizes the spatial correlation and consistent shape in chest anatomy. We hope DigitAnatomy can prompt the development, evaluation, and interpretability of anomaly detection methods.

The increasing interest in developing Artificial Intelligence applications in the medical domain, suffers from the lack of high-quality dataset, mainly due to privacy-related issues. Moreover, the recent rising of Multimodal Large Language Models (MLLM) leads to a need for multimodal medical datasets, where clinical reports and findings are attached to the corresponding CT or MR scans. This paper illustrates the entire workflow for building the data set MedPix 2.0. Starting from the well-known multimodal dataset MedPix\textregistered, mainly used by physicians, nurses and healthcare students for Continuing Medical Education purposes, a semi-automatic pipeline was developed to extract visual and textual data followed by a manual curing procedure where noisy samples were removed, thus creating a MongoDB database. Along with the dataset, we developed a GUI aimed at navigating efficiently the MongoDB instance, and obtaining the raw data that can be easily used for training and/or fine-tuning MLLMs. To enforce this point, we also propose a CLIP-based model trained on MedPix 2.0 for scan classification tasks.

Medical report generation from X-ray images is a challenging task, particularly in an unpaired setting where paired image-report data is unavailable for training. To address this challenge, we propose a novel model that leverages the available information in two distinct datasets, one comprising reports and the other consisting of images. The core idea of our model revolves around the notion that combining auto-encoding report generation with multi-modal (report-image) alignment can offer a solution. However, the challenge persists regarding how to achieve this alignment when pair correspondence is absent. Our proposed solution involves the use of auxiliary tasks, particularly contrastive learning and classification, to position related images and reports in close proximity to each other. This approach differs from previous methods that rely on pre-processing steps, such as using external information stored in a knowledge graph. Our model, named MedRAT, surpasses previous state-of-the-art methods, demonstrating the feasibility of generating comprehensive medical reports without the need for paired data or external tools.

Medical imaging analysis plays a critical role in the diagnosis and treatment of various medical conditions. This paper focuses on chest X-ray images and their corresponding radiological reports. It presents a new model that learns a joint X-ray image & report representation. The model is based on a novel alignment scheme between the visual data and the text, which takes into account both local and global information. Furthermore, the model integrates domain-specific information of two types -- lateral images and the consistent visual structure of chest images. Our representation is shown to benefit three types of retrieval tasks: text-image retrieval, class-based retrieval, and phrase-grounding.

The field of Machine Learning, a subset of Artificial Intelligence, has led to remarkable advancements in many areas, including medicine. Machine Learning algorithms require large datasets to train computer models successfully. Although there are medical image datasets available, more image datasets are needed from a variety of medical entities, especially cancer pathology. Even more scarce are ML-ready image datasets. To address this need, we created an image dataset (LC25000) with 25,000 color images in 5 classes. Each class contains 5,000 images of the following histologic entities: colon adenocarcinoma, benign colonic tissue, lung adenocarcinoma, lung squamous cell carcinoma, and benign lung tissue. All images are de-identified, HIPAA compliant, validated, and freely available for download to AI researchers.

Automated structured radiology report generation (SRRG) from chest X-ray images offers significant potential to reduce workload of radiologists by generating reports in structured formats that ensure clarity, consistency, and adherence to clinical reporting standards. While radiologists effectively utilize available clinical contexts in their diagnostic reasoning, existing SRRG systems overlook these essential elements. This fundamental gap leads to critical problems including temporal hallucinations when referencing non-existent clinical contexts. To address these limitations, we propose contextualized SRRG (C-SRRG) that comprehensively incorporates rich clinical context for SRRG. We curate C-SRRG dataset by integrating comprehensive clinical context encompassing 1) multi-view X-ray images, 2) clinical indication, 3) imaging techniques, and 4) prior studies with corresponding comparisons based on patient histories. Through extensive benchmarking with state-of-the-art multimodal large language models, we demonstrate that incorporating clinical context with the proposed C-SRRG significantly improves report generation quality. We publicly release dataset, code, and checkpoints to facilitate future research for clinically-aligned automated RRG at https://github.com/vuno/contextualized-srrg.

Most of the existing chest X-ray datasets include labels from a list of findings without specifying their locations on the radiographs. This limits the development of machine learning algorithms for the detection and localization of chest abnormalities. In this work, we describe a dataset of more than 100,000 chest X-ray scans that were retrospectively collected from two major hospitals in Vietnam. Out of this raw data, we release 18,000 images that were manually annotated by a total of 17 experienced radiologists with 22 local labels of rectangles surrounding abnormalities and 6 global labels of suspected diseases. The released dataset is divided into a training set of 15,000 and a test set of 3,000. Each scan in the training set was independently labeled by 3 radiologists, while each scan in the test set was labeled by the consensus of 5 radiologists. We designed and built a labeling platform for DICOM images to facilitate these annotation procedures. All images are made publicly available (https://www.physionet.org/content/vindr-cxr/1.0.0/) in DICOM format along with the labels of both the training set and the test set.

Deep neural networks have brought remarkable breakthroughs in medical image analysis. However, due to their data-hungry nature, the modest dataset sizes in medical imaging projects might be hindering their full potential. Generating synthetic data provides a promising alternative, allowing to complement training datasets and conducting medical image research at a larger scale. Diffusion models recently have caught the attention of the computer vision community by producing photorealistic synthetic images. In this study, we explore using Latent Diffusion Models to generate synthetic images from high-resolution 3D brain images. We used T1w MRI images from the UK Biobank dataset (N=31,740) to train our models to learn about the probabilistic distribution of brain images, conditioned on covariables, such as age, sex, and brain structure volumes. We found that our models created realistic data, and we could use the conditioning variables to control the data generation effectively. Besides that, we created a synthetic dataset with 100,000 brain images and made it openly available to the scientific community.

Artificial intelligence-assisted imaging analysis has made substantial strides in tumor diagnosis and management. Here we present PASTA, a pan-tumor CT foundation model that achieves state-of-the-art performance on 45 of 46 representative oncology tasks -- including lesion segmentation, tumor detection in plain CT, tumor staging, survival prediction, structured report generation, and cross-modality transfer learning, significantly outperforming the second-best models on 35 tasks. This remarkable advancement is driven by our development of PASTA-Gen, an innovative synthetic tumor generation framework that produces a comprehensive dataset of 30,000 CT scans with pixel-level annotated lesions and paired structured reports, encompassing malignancies across ten organs and five benign lesion types. By leveraging this rich, high-quality synthetic data, we overcome a longstanding bottleneck in the development of CT foundation models -- specifically, the scarcity of publicly available, high-quality annotated datasets due to privacy constraints and the substantial labor required for scaling precise data annotation. Encouragingly, PASTA demonstrates exceptional data efficiency with promising practical value, markedly improving performance on various tasks with only a small amount of real-world data. The open release of both the synthetic dataset and PASTA foundation model effectively addresses the challenge of data scarcity, thereby advancing oncological research and clinical translation.

Non-ideal measurement computed tomography (NICT), which sacrifices optimal imaging standards for new advantages in CT imaging, is expanding the clinical application scope of CT images. However, with the reduction of imaging standards, the image quality has also been reduced, extremely limiting the clinical acceptability. Although numerous studies have demonstrated the feasibility of deep learning for the NICT enhancement in specific scenarios, their high data cost and limited generalizability have become large obstacles. The recent research on the foundation model has brought new opportunities for building a universal NICT enhancement model - bridging the image quality degradation with minimal data cost. However, owing to the challenges in the collection of large pre-training datasets and the compatibility of data variation, no success has been reported. In this paper, we propose a multi-scale integrated Transformer AMPlifier (TAMP), the first imaging foundation model for universal NICT enhancement. It has been pre-trained on a large-scale physical-driven simulation dataset with 3.6 million NICT-ICT image pairs, and is able to directly generalize to the NICT enhancement tasks with various non-ideal settings and body regions. Via the adaptation with few data, it can further achieve professional performance in real-world specific scenarios. Our extensive experiments have demonstrated that the proposed TAMP has significant potential for promoting the exploration and application of NICT and serving a wider range of medical scenarios.

Plankton recognition provides novel possibilities to study various environmental aspects and an interesting real-world context to develop domain adaptation (DA) methods. Different imaging instruments cause domain shift between datasets hampering the development of general plankton recognition methods. A promising remedy for this is DA allowing to adapt a model trained on one instrument to other instruments. In this paper, we present a new DA dataset called DAPlankton which consists of phytoplankton images obtained with different instruments. Phytoplankton provides a challenging DA problem due to the fine-grained nature of the task and high class imbalance in real-world datasets. DAPlankton consists of two subsets. DAPlankton_LAB contains images of cultured phytoplankton providing a balanced dataset with minimal label uncertainty. DAPlankton_SEA consists of images collected from the Baltic Sea providing challenging real-world data with large intra-class variance and class imbalance. We further present a benchmark comparison of three widely used DA methods.

Radiology reports convey detailed clinical observations and capture diagnostic reasoning that evolves over time. However, existing evaluation methods are limited to single-report settings and rely on coarse metrics that fail to capture fine-grained clinical semantics and temporal dependencies. We introduce LUNGUAGE,a benchmark dataset for structured radiology report generation that supports both single-report evaluation and longitudinal patient-level assessment across multiple studies. It contains 1,473 annotated chest X-ray reports, each reviewed by experts, and 80 of them contain longitudinal annotations to capture disease progression and inter-study intervals, also reviewed by experts. Using this benchmark, we develop a two-stage framework that transforms generated reports into fine-grained, schema-aligned structured representations, enabling longitudinal interpretation. We also propose LUNGUAGESCORE, an interpretable metric that compares structured outputs at the entity, relation, and attribute level while modeling temporal consistency across patient timelines. These contributions establish the first benchmark dataset, structuring framework, and evaluation metric for sequential radiology reporting, with empirical results demonstrating that LUNGUAGESCORE effectively supports structured report evaluation. The code is available at: https://github.com/SuperSupermoon/Lunguage

Deep learning has revolutionized medical imaging, but its effectiveness is severely limited by insufficient labeled training data. This paper introduces a novel GAN-based semi-supervised learning framework specifically designed for low labeled-data regimes, evaluated across settings with 5 to 50 labeled samples per class. Our approach integrates three specialized neural networks -- a generator for class-conditioned image translation, a discriminator for authenticity assessment and classification, and a dedicated classifier -- within a three-phase training framework. The method alternates between supervised training on limited labeled data and unsupervised learning that leverages abundant unlabeled images through image-to-image translation rather than generation from noise. We employ ensemble-based pseudo-labeling that combines confidence-weighted predictions from the discriminator and classifier with temporal consistency through exponential moving averaging, enabling reliable label estimation for unlabeled data. Comprehensive evaluation across eleven MedMNIST datasets demonstrates that our approach achieves statistically significant improvements over six state-of-the-art GAN-based semi-supervised methods, with particularly strong performance in the extreme 5-shot setting where the scarcity of labeled data is most challenging. The framework maintains its superiority across all evaluated settings (5, 10, 20, and 50 shots per class). Our approach offers a practical solution for medical imaging applications where annotation costs are prohibitive, enabling robust classification performance even with minimal labeled data. Code is available at https://github.com/GuidoManni/SPARSE.

The diffusion MRI Neurite Exchange Imaging model offers a promising framework for probing gray matter microstructure by estimating parameters such as compartment sizes, diffusivities, and inter-compartmental water exchange time. However, existing protocols require long scan times. This study proposes a reduced acquisition scheme for the Connectome 2.0 scanner that preserves model accuracy while substantially shortening scan duration. We developed a data-driven framework using explainable artificial intelligence with a guided recursive feature elimination strategy to identify an optimal 8-feature subset from a 15-feature protocol. The performance of this optimized protocol was validated in vivo and benchmarked against the full acquisition and alternative reduction strategies. Parameter accuracy, preservation of anatomical contrast, and test-retest reproducibility were assessed. The reduced protocol yielded parameter estimates and cortical maps comparable to the full protocol, with low estimation errors in synthetic data and minimal impact on test-retest variability. Compared to theory-driven and heuristic reduction schemes, the optimized protocol demonstrated superior robustness, reducing the deviation in water exchange time estimates by over two-fold. In conclusion, this hybrid optimization framework enables viable imaging of neurite exchange in 14 minutes without loss of parameter fidelity. This approach supports the broader application of exchange-sensitive diffusion magnetic resonance imaging in neuroscience and clinical research, and offers a generalizable method for designing efficient acquisition protocols in biophysical parameter mapping.

Spine-related diseases have high morbidity and cause a huge burden of social cost. Spine imaging is an essential tool for noninvasively visualizing and assessing spinal pathology. Segmenting vertebrae in computed tomography (CT) images is the basis of quantitative medical image analysis for clinical diagnosis and surgery planning of spine diseases. Current publicly available annotated datasets on spinal vertebrae are small in size. Due to the lack of a large-scale annotated spine image dataset, the mainstream deep learning-based segmentation methods, which are data-driven, are heavily restricted. In this paper, we introduce a large-scale spine CT dataset, called CTSpine1K, curated from multiple sources for vertebra segmentation, which contains 1,005 CT volumes with over 11,100 labeled vertebrae belonging to different spinal conditions. Based on this dataset, we conduct several spinal vertebrae segmentation experiments to set the first benchmark. We believe that this large-scale dataset will facilitate further research in many spine-related image analysis tasks, including but not limited to vertebrae segmentation, labeling, 3D spine reconstruction from biplanar radiographs, image super-resolution, and enhancement.

Data augmentation is essential in medical imaging for improving classification accuracy, lesion detection, and organ segmentation under limited data conditions. However, two significant challenges remain. First, a pronounced domain gap between natural photographs and medical images can distort critical disease features. Second, augmentation studies in medical imaging are fragmented and limited to single tasks or architectures, leaving the benefits of advanced mix-based strategies unclear. To address these challenges, we propose a unified evaluation framework with six mix-based augmentation methods integrated with both convolutional and transformer backbones on brain tumour MRI and eye disease fundus datasets. Our contributions are threefold. (1) We introduce MediAug, a comprehensive and reproducible benchmark for advanced data augmentation in medical imaging. (2) We systematically evaluate MixUp, YOCO, CropMix, CutMix, AugMix, and SnapMix with ResNet-50 and ViT-B backbones. (3) We demonstrate through extensive experiments that MixUp yields the greatest improvement on the brain tumor classification task for ResNet-50 with 79.19% accuracy and SnapMix yields the greatest improvement for ViT-B with 99.44% accuracy, and that YOCO yields the greatest improvement on the eye disease classification task for ResNet-50 with 91.60% accuracy and CutMix yields the greatest improvement for ViT-B with 97.94% accuracy. Code will be available at https://github.com/AIGeeksGroup/MediAug.

This work addresses image restoration tasks through the lens of inverse problems using unpaired datasets. In contrast to traditional approaches -- which typically assume full knowledge of the forward model or access to paired degraded and ground-truth images -- the proposed method operates under minimal assumptions and relies only on small, unpaired datasets. This makes it particularly well-suited for real-world scenarios, where the forward model is often unknown or misspecified, and collecting paired data is costly or infeasible. The method leverages conditional flow matching to model the distribution of degraded observations, while simultaneously learning the forward model via a distribution-matching loss that arises naturally from the framework. Empirically, it outperforms both single-image blind and unsupervised approaches on deblurring and non-uniform point spread function (PSF) calibration tasks. It also matches state-of-the-art performance on blind super-resolution. We also showcase the effectiveness of our method with a proof of concept for lens calibration: a real-world application traditionally requiring time-consuming experiments and specialized equipment. In contrast, our approach achieves this with minimal data acquisition effort.

Medical imaging analysis faces challenges such as data scarcity, high annotation costs, and privacy concerns. This paper introduces the Medical AI for Synthetic Imaging (MAISI), an innovative approach using the diffusion model to generate synthetic 3D computed tomography (CT) images to address those challenges. MAISI leverages the foundation volume compression network and the latent diffusion model to produce high-resolution CT images (up to a landmark volume dimension of 512 x 512 x 768 ) with flexible volume dimensions and voxel spacing. By incorporating ControlNet, MAISI can process organ segmentation, including 127 anatomical structures, as additional conditions and enables the generation of accurately annotated synthetic images that can be used for various downstream tasks. Our experiment results show that MAISI's capabilities in generating realistic, anatomically accurate images for diverse regions and conditions reveal its promising potential to mitigate challenges using synthetic data.

The increase in non-biodegradable waste is a worldwide concern. Recycling facilities play a crucial role, but their automation is hindered by the complex characteristics of waste recycling lines like clutter or object deformation. In addition, the lack of publicly available labeled data for these environments makes developing robust perception systems challenging. Our work explores the benefits of multimodal perception for object segmentation in real waste management scenarios. First, we present SpectralWaste, the first dataset collected from an operational plastic waste sorting facility that provides synchronized hyperspectral and conventional RGB images. This dataset contains labels for several categories of objects that commonly appear in sorting plants and need to be detected and separated from the main trash flow for several reasons, such as security in the management line or reuse. Additionally, we propose a pipeline employing different object segmentation architectures and evaluate the alternatives on our dataset, conducting an extensive analysis for both multimodal and unimodal alternatives. Our evaluation pays special attention to efficiency and suitability for real-time processing and demonstrates how HSI can bring a boost to RGB-only perception in these realistic industrial settings without much computational overhead.

Diffusion models have become a popular approach for image generation and reconstruction due to their numerous advantages. However, most diffusion-based inverse problem-solving methods only deal with 2D images, and even recently published 3D methods do not fully exploit the 3D distribution prior. To address this, we propose a novel approach using two perpendicular pre-trained 2D diffusion models to solve the 3D inverse problem. By modeling the 3D data distribution as a product of 2D distributions sliced in different directions, our method effectively addresses the curse of dimensionality. Our experimental results demonstrate that our method is highly effective for 3D medical image reconstruction tasks, including MRI Z-axis super-resolution, compressed sensing MRI, and sparse-view CT. Our method can generate high-quality voxel volumes suitable for medical applications.

This paper presents an annotated dataset of brain MRI images designed to advance the field of brain symmetry study. Magnetic resonance imaging (MRI) has gained interest in analyzing brain symmetry in neonatal infants, and challenges remain due to the vast size differences between fetal and adult brains. Classification methods for brain structural MRI use scales and visual cues to assess hemisphere symmetry, which can help diagnose neonatal patients by comparing hemispheres and anatomical regions of interest in the brain. Using the Developing Human Connectome Project dataset, this work presents a dataset comprising cerebral images extracted as slices across selected portions of interest for clinical evaluation . All the extracted images are annotated with the brain's midline. All the extracted images are annotated with the brain's midline. From the assumption that a decrease in symmetry is directly related to possible clinical pathologies, the dataset can contribute to a more precise diagnosis because it can be used to train deep learning model application in neonatal cerebral MRI anomaly detection from postnatal infant scans thanks to computer vision. Such models learn to identify and classify anomalies by identifying potential asymmetrical patterns in medical MRI images. Furthermore, this dataset can contribute to the research and development of methods using the relative symmetry of the two brain hemispheres for crucial diagnosis and treatment planning.

This paper introduces a high resolution, machine learning-ready heliophysics dataset derived from NASA's Solar Dynamics Observatory (SDO), specifically designed to advance machine learning (ML) applications in solar physics and space weather forecasting. The dataset includes processed imagery from the Atmospheric Imaging Assembly (AIA) and Helioseismic and Magnetic Imager (HMI), spanning a solar cycle from May 2010 to July 2024. To ensure suitability for ML tasks, the data has been preprocessed, including correction of spacecraft roll angles, orbital adjustments, exposure normalization, and degradation compensation. We also provide auxiliary application benchmark datasets complementing the core SDO dataset. These provide benchmark applications for central heliophysics and space weather tasks such as active region segmentation, active region emergence forecasting, coronal field extrapolation, solar flare prediction, solar EUV spectra prediction, and solar wind speed estimation. By establishing a unified, standardized data collection, this dataset aims to facilitate benchmarking, enhance reproducibility, and accelerate the development of AI-driven models for critical space weather prediction tasks, bridging gaps between solar physics, machine learning, and operational forecasting.

Recent advancements in prompt-based medical image segmentation have enabled clinicians to identify tumors using simple input like bounding boxes or text prompts. However, existing methods face challenges when doctors need to interact through natural language or when position reasoning is required - understanding spatial relationships between anatomical structures and pathologies. We present PRS-Med, a framework that integrates vision-language models with segmentation capabilities to generate both accurate segmentation masks and corresponding spatial reasoning outputs. Additionally, we introduce the MMRS dataset (Multimodal Medical in Positional Reasoning Segmentation), which provides diverse, spatially-grounded question-answer pairs to address the lack of position reasoning data in medical imaging. PRS-Med demonstrates superior performance across six imaging modalities (CT, MRI, X-ray, ultrasound, endoscopy, RGB), significantly outperforming state-of-the-art methods in both segmentation accuracy and position reasoning. Our approach enables intuitive doctor-system interaction through natural language, facilitating more efficient diagnoses. Our dataset pipeline, model, and codebase will be released to foster further research in spatially-aware multimodal reasoning for medical applications.

Reflection removal is challenging due to complex light interactions, where reflections obscure important details and hinder scene understanding. Polarization naturally provides a powerful cue to distinguish between reflected and transmitted light, enabling more accurate reflection removal. However, existing methods often rely on small-scale or synthetic datasets, which fail to capture the diversity and complexity of real-world scenarios. To this end, we construct a large-scale dataset, PolaRGB, for Polarization-based reflection removal of RGB images, which enables us to train models that generalize effectively across a wide range of real-world scenarios. The PolaRGB dataset contains 6,500 well-aligned mixed-transmission image pairs, 8x larger than existing polarization datasets, and is the first to include both RGB and polarization images captured across diverse indoor and outdoor environments with varying lighting conditions. Besides, to fully exploit the potential of polarization cues for reflection removal, we introduce PolarFree, which leverages diffusion process to generate reflection-free cues for accurate reflection removal. Extensive experiments show that PolarFree significantly enhances image clarity in challenging reflective scenarios, setting a new benchmark for polarized imaging and reflection removal. Code and dataset are available at https://github.com/mdyao/PolarFree.

Brain tumor growth is unique to each glioma patient and extends beyond what is visible in imaging scans, infiltrating surrounding brain tissue. Understanding these hidden patient-specific progressions is essential for effective therapies. Current treatment plans for brain tumors, such as radiotherapy, typically involve delineating a uniform margin around the visible tumor on pre-treatment scans to target this invisible tumor growth. This "one size fits all" approach is derived from population studies and often fails to account for the nuances of individual patient conditions. We present the GliODIL framework, which infers the full spatial distribution of tumor cell concentration from available multi-modal imaging, leveraging a Fisher-Kolmogorov type physics model to describe tumor growth. This is achieved through the newly introduced method of Optimizing the Discrete Loss (ODIL), where both data and physics-based constraints are softly assimilated into the solution. Our test dataset comprises 152 glioblastoma patients with pre-treatment imaging and post-treatment follow-ups for tumor recurrence monitoring. By blending data-driven techniques with physics-based constraints, GliODIL enhances recurrence prediction in radiotherapy planning, challenging traditional uniform margins and strict adherence to the Fisher-Kolmogorov partial differential equation (PDE) model, which is adapted for complex cases.

This paper presents the winning solution of task 1 and the third-placed solution of task 3 of the BraTS challenge. The use of automated tools in clinical practice has increased due to the development of more and more sophisticated and reliable algorithms. However, achieving clinical standards and developing tools for real-life scenarios is a major challenge. To this end, BraTS has organised tasks to find the most advanced solutions for specific purposes. In this paper, we propose the use of synthetic data to train state-of-the-art frameworks in order to improve the segmentation of adult gliomas in a post-treatment scenario, and the segmentation of meningioma for radiotherapy planning. Our results suggest that the use of synthetic data leads to more robust algorithms, although the synthetic data generation pipeline is not directly suited to the meningioma task. In task 1, we achieved a DSC of 0.7900, 0.8076, 0.7760, 0.8926, 0.7874, 0.8938 and a HD95 of 35.63, 30.35, 44.58, 16.87, 38.19, 17.95 for ET, NETC, RC, SNFH, TC and WT, respectively and, in task 3, we achieved a DSC of 0.801 and HD95 of 38.26, in the testing phase. The code for these tasks is available at https://github.com/ShadowTwin41/BraTS_2023_2024_solutions.

The ability to recover MRI signal from noise is key to achieve fast acquisition, accurate quantification, and high image quality. Past work has shown convolutional neural networks can be used with abundant and paired low and high-SNR images for training. However, for applications where high-SNR data is difficult to produce at scale (e.g. with aggressive acceleration, high resolution, or low field strength), training a new denoising network using a large quantity of high-SNR images can be infeasible. In this study, we overcome this limitation by improving the generalization of denoising models, enabling application to many settings beyond what appears in the training data. Specifically, we a) develop a training scheme that uses complex MRIs reconstructed in the SNR units (i.e., the images have a fixed noise level, SNR unit training) and augments images with realistic noise based on coil g-factor, and b) develop a novel imaging transformer (imformer) to handle 2D, 2D+T, and 3D MRIs in one model architecture. Through empirical evaluation, we show this combination improves performance compared to CNN models and improves generalization, enabling a denoising model to be used across field-strengths, image contrasts, and anatomy.

Half of the JWST high-contrast imaging objects will only have photometric data {{as of Cycle 2}}. However, to better understand their atmospheric chemistry which informs formation origin, spectroscopic data are preferred. Using HIP 65426 b, we investigate to what extent planet properties and atmospheric chemical abundance can be retrieved with only JWST photometric data points (2.5-15.5 mum) in conjunction with ground-based archival low-resolution spectral data (1.0-2.3 mum). We find that the data is consistent with an atmosphere with solar metallicity and C/O ratios at 0.40 and 0.55. We rule out 10x solar metallicity and an atmosphere with C/O = 1.0. We also find strong evidence of silicate clouds but no sign of an enshrouding featureless {{dust}} extinction. This work offers guidance and cautionary tales on analyzing data in the absence of medium-to-high resolution spectral data.

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

The DESI Legacy Imaging Surveys are a combination of three public projects (the Dark Energy Camera Legacy Survey, the Beijing-Arizona Sky Survey, and the Mayall z-band Legacy Survey) that will jointly image approximately 14,000 deg^2 of the extragalactic sky visible from the northern hemisphere in three optical bands (g, r, and z) using telescopes at the Kitt Peak National Observatory and the Cerro Tololo Inter-American Observatory. The combined survey footprint is split into two contiguous areas by the Galactic plane. The optical imaging is conducted using a unique strategy of dynamically adjusting the exposure times and pointing selection during observing that results in a survey of nearly uniform depth. In addition to calibrated images, the project is delivering a catalog, constructed by using a probabilistic inference-based approach to estimate source shapes and brightnesses. The catalog includes photometry from the grz optical bands and from four mid-infrared bands (at 3.4, 4.6, 12 and 22 micorons) observed by the Wide-field Infrared Survey Explorer (WISE) satellite during its full operational lifetime. The project plans two public data releases each year. All the software used to generate the catalogs is also released with the data. This paper provides an overview of the Legacy Surveys project.

The Computer Vision Research Lab at the University of Notre Dame began collecting iris images in the spring semester of 2004. The initial data collections used an LG 2200 iris imaging system for image acquisition. Image datasets acquired in 2004-2005 at Notre Dame with this LG 2200 have been used in the ICE 2005 and ICE 2006 iris biometric evaluations. The ICE 2005 iris image dataset has been distributed to over 100 research groups around the world. The purpose of this document is to describe the content of the ND-IRIS-0405 iris image dataset. This dataset is a superset of the iris image datasets used in ICE 2005 and ICE 2006. The ND 2004-2005 iris image dataset contains 64,980 images corresponding to 356 unique subjects, and 712 unique irises. The age range of the subjects is 18 to 75 years old. 158 of the subjects are female, and 198 are male. 250 of the subjects are Caucasian, 82 are Asian, and 24 are other ethnicities.

Current autonomous driving algorithms heavily rely on the visible spectrum, which is prone to performance degradation in adverse conditions like fog, rain, snow, glare, and high contrast. Although other spectral bands like near-infrared (NIR) and long-wave infrared (LWIR) can enhance vision perception in such situations, they have limitations and lack large-scale datasets and benchmarks. Short-wave infrared (SWIR) imaging offers several advantages over NIR and LWIR. However, no publicly available large-scale datasets currently incorporate SWIR data for autonomous driving. To address this gap, we introduce the RGB and SWIR Multispectral Driving (RASMD) dataset, which comprises 100,000 synchronized and spatially aligned RGB-SWIR image pairs collected across diverse locations, lighting, and weather conditions. In addition, we provide a subset for RGB-SWIR translation and object detection annotations for a subset of challenging traffic scenarios to demonstrate the utility of SWIR imaging through experiments on both object detection and RGB-to-SWIR image translation. Our experiments show that combining RGB and SWIR data in an ensemble framework significantly improves detection accuracy compared to RGB-only approaches, particularly in conditions where visible-spectrum sensors struggle. We anticipate that the RASMD dataset will advance research in multispectral imaging for autonomous driving and robust perception systems.

Berry picking has long-standing traditions in Finland, yet it is challenging and can potentially be dangerous. The integration of drones equipped with advanced imaging techniques represents a transformative leap forward, optimising harvests and promising sustainable practices. We propose WildBe, the first image dataset of wild berries captured in peatlands and under the canopy of Finnish forests using drones. Unlike previous and related datasets, WildBe includes new varieties of berries, such as bilberries, cloudberries, lingonberries, and crowberries, captured under severe light variations and in cluttered environments. WildBe features 3,516 images, including a total of 18,468 annotated bounding boxes. We carry out a comprehensive analysis of WildBe using six popular object detectors, assessing their effectiveness in berry detection across different forest regions and camera types. We will release WildBe publicly.

Chest Xray imaging is a widely used diagnostic tool in modern medicine, and its high utilization creates substantial workloads for radiologists. To alleviate this burden, vision language models are increasingly applied to automate Chest Xray radiology report generation (CXRRRG), aiming for clinically accurate descriptions while reducing manual effort. Conventional approaches, however, typically rely on single images, failing to capture the longitudinal context necessary for producing clinically faithful comparison statements. Recently, growing attention has been directed toward incorporating longitudinal data into CXR RRG, enabling models to leverage historical studies in ways that mirror radiologists diagnostic workflows. Nevertheless, existing surveys primarily address single image CXRRRG and offer limited guidance for longitudinal settings, leaving researchers without a systematic framework for model design. To address this gap, this survey provides the first comprehensive review of longitudinal radiology report generation (LRRG). Specifically, we examine dataset construction strategies, report generation architectures alongside longitudinally tailored designs, and evaluation protocols encompassing both longitudinal specific measures and widely used benchmarks. We further summarize LRRG methods performance, alongside analyses of different ablation studies, which collectively highlight the critical role of longitudinal information and architectural design choices in improving model performance. Finally, we summarize five major limitations of current research and outline promising directions for future development, aiming to lay a foundation for advancing this emerging field.

Fairness remains a critical concern in healthcare, where unequal access to services and treatment outcomes can adversely affect patient health. While Federated Learning (FL) presents a collaborative and privacy-preserving approach to model training, ensuring fairness is challenging due to heterogeneous data across institutions, and current research primarily addresses non-medical applications. To fill this gap, we establish the first experimental benchmark for fairness in medical FL, evaluating six representative FL methods across diverse demographic attributes and imaging modalities. We introduce FairFedMed, the first medical FL dataset specifically designed to study group fairness (i.e., demographics). It comprises two parts: FairFedMed-Oph, featuring 2D fundus and 3D OCT ophthalmology samples with six demographic attributes; and FairFedMed-Chest, which simulates real cross-institutional FL using subsets of CheXpert and MIMIC-CXR. Together, they support both simulated and real-world FL across diverse medical modalities and demographic groups. Existing FL models often underperform on medical images and overlook fairness across demographic groups. To address this, we propose FairLoRA, a fairness-aware FL framework based on SVD-based low-rank approximation. It customizes singular value matrices per demographic group while sharing singular vectors, ensuring both fairness and efficiency. Experimental results on the FairFedMed dataset demonstrate that FairLoRA not only achieves state-of-the-art performance in medical image classification but also significantly improves fairness across diverse populations. Our code and dataset can be accessible via link: https://wang.hms.harvard.edu/fairfedmed/.

Deep learning (DL), a pivotal technology in artificial intelligence, has recently gained substantial traction in the domain of dental auxiliary diagnosis. However, its application has predominantly been confined to imaging modalities such as panoramic radiographs and Cone Beam Computed Tomography, with limited focus on auxiliary analysis specifically targeting Periapical Radiographs (PR). PR are the most extensively utilized imaging modality in endodontics and periodontics due to their capability to capture detailed local lesions at a low cost. Nevertheless, challenges such as resolution limitations and artifacts complicate the annotation and recognition of PR, leading to a scarcity of publicly available, large-scale, high-quality PR analysis datasets. This scarcity has somewhat impeded the advancement of DL applications in PR analysis. In this paper, we present PRAD-10K, a dataset for PR analysis. PRAD-10K comprises 10,000 clinical periapical radiograph images, with pixel-level annotations provided by professional dentists for nine distinct anatomical structures, lesions, and artificial restorations or medical devices, We also include classification labels for images with typical conditions or lesions. Furthermore, we introduce a DL network named PRNet to establish benchmarks for PR segmentation tasks. Experimental results demonstrate that PRNet surpasses previous state-of-the-art medical image segmentation models on the PRAD-10K dataset. The codes and dataset will be made publicly available.

Self-supervised learning (SSL) has emerged as a promising paradigm in medical imaging, addressing the chronic challenge of limited labeled data in healthcare settings. While SSL has shown impressive results, existing studies in the medical domain are often limited in scope, focusing on specific datasets or modalities, or evaluating only isolated aspects of model performance. This fragmented evaluation approach poses a significant challenge, as models deployed in critical medical settings must not only achieve high accuracy but also demonstrate robust performance and generalizability across diverse datasets and varying conditions. To address this gap, we present a comprehensive evaluation of SSL methods within the medical domain, with a particular focus on robustness and generalizability. Using the MedMNIST dataset collection as a standardized benchmark, we evaluate 8 major SSL methods across 11 different medical datasets. Our study provides an in-depth analysis of model performance in both in-domain scenarios and the detection of out-of-distribution (OOD) samples, while exploring the effect of various initialization strategies, model architectures, and multi-domain pre-training. We further assess the generalizability of SSL methods through cross-dataset evaluations and the in-domain performance with varying label proportions (1%, 10%, and 100%) to simulate real-world scenarios with limited supervision. We hope this comprehensive benchmark helps practitioners and researchers make more informed decisions when applying SSL methods to medical applications.

Influenced by the complexity of volumetric imaging, there is a shortage of established datasets useful for benchmarking volumetric deep-learning models. As a consequence, new and existing models are not easily comparable, limiting the development of architectures optimized specifically for volumetric data. To counteract this trend, we introduce MozzaVID - a large, clean, and versatile volumetric classification dataset. Our dataset contains X-ray computed tomography (CT) images of mozzarella microstructure and enables the classification of 25 cheese types and 149 cheese samples. We provide data in three different resolutions, resulting in three dataset instances containing from 591 to 37,824 images. While being general-purpose, the dataset also facilitates investigating mozzarella structure properties. The structure of food directly affects its functional properties and thus its consumption experience. Understanding food structure helps tune the production and mimicking it enables sustainable alternatives to animal-derived food products. The complex and disordered nature of food structures brings a unique challenge, where a choice of appropriate imaging method, scale, and sample size is not trivial. With this dataset we aim to address these complexities, contributing to more robust structural analysis models. The dataset can be downloaded from: https://archive.compute.dtu.dk/files/public/projects/MozzaVID/.

Confocal fluorescence microscopy is one of the most accessible and widely used imaging techniques for the study of biological processes. Scanning confocal microscopy allows the capture of high-quality images from 3D samples, yet suffers from well-known limitations such as photobleaching and phototoxicity of specimens caused by intense light exposure, which limits its use in some applications, especially for living cells. Cellular damage can be alleviated by changing imaging parameters to reduce light exposure, often at the expense of image quality. Machine/deep learning methods for single-image super-resolution (SISR) can be applied to restore image quality by upscaling lower-resolution (LR) images to produce high-resolution images (HR). These SISR methods have been successfully applied to photo-realistic images due partly to the abundance of publicly available data. In contrast, the lack of publicly available data partly limits their application and success in scanning confocal microscopy. In this paper, we introduce a large scanning confocal microscopy dataset named SR-CACO-2 that is comprised of low- and high-resolution image pairs marked for three different fluorescent markers. It allows the evaluation of performance of SISR methods on three different upscaling levels (X2, X4, X8). SR-CACO-2 contains the human epithelial cell line Caco-2 (ATCC HTB-37), and it is composed of 22 tiles that have been translated in the form of 9,937 image patches for experiments with SISR methods. Given the new SR-CACO-2 dataset, we also provide benchmarking results for 15 state-of-the-art methods that are representative of the main SISR families. Results show that these methods have limited success in producing high-resolution textures, indicating that SR-CACO-2 represents a challenging problem. Our dataset, code and pretrained weights are available: https://github.com/sbelharbi/sr-caco-2.

In this paper, we introduce StreakNet-Arch, a novel signal processing architecture designed for Underwater Carrier LiDAR-Radar (UCLR) imaging systems, to address the limitations in scatter suppression and real-time imaging. StreakNet-Arch formulates the signal processing as a real-time, end-to-end binary classification task, enabling real-time image acquisition. To achieve this, we leverage Self-Attention networks and propose a novel Double Branch Cross Attention (DBC-Attention) mechanism that surpasses the performance of traditional methods. Furthermore, we present a method for embedding streak-tube camera images into attention networks, effectively acting as a learned bandpass filter. To facilitate further research, we contribute a publicly available streak-tube camera image dataset. The dataset contains 2,695,168 real-world underwater 3D point cloud data. These advancements significantly improve UCLR capabilities, enhancing its performance and applicability in underwater imaging tasks. The source code and dataset can be found at https://github.com/BestAnHongjun/StreakNet .

This work summarizes the results of the largest skin image analysis challenge in the world, hosted by the International Skin Imaging Collaboration (ISIC), a global partnership that has organized the world's largest public repository of dermoscopic images of skin. The challenge was hosted in 2018 at the Medical Image Computing and Computer Assisted Intervention (MICCAI) conference in Granada, Spain. The dataset included over 12,500 images across 3 tasks. 900 users registered for data download, 115 submitted to the lesion segmentation task, 25 submitted to the lesion attribute detection task, and 159 submitted to the disease classification task. Novel evaluation protocols were established, including a new test for segmentation algorithm performance, and a test for algorithm ability to generalize. Results show that top segmentation algorithms still fail on over 10% of images on average, and algorithms with equal performance on test data can have different abilities to generalize. This is an important consideration for agencies regulating the growing set of machine learning tools in the healthcare domain, and sets a new standard for future public challenges in healthcare.

Planktonic organisms are of fundamental importance to marine ecosystems: they form the basis of the food web, provide the link between the atmosphere and the deep ocean, and influence global-scale biogeochemical cycles. Scientists are increasingly using imaging-based technologies to study these creatures in their natural habit. Images from such systems provide an unique opportunity to model and understand plankton ecosystems, but the collected datasets can be enormous. The Imaging FlowCytobot (IFCB) at Woods Hole Oceanographic Institution, for example, is an in situ system that has been continuously imaging plankton since 2006. To date, it has generated more than 700 million samples. Manual classification of such a vast image collection is impractical due to the size of the data set. In addition, the annotation task is challenging due to the large space of relevant classes, intra-class variability, and inter-class similarity. Methods for automated classification exist, but the accuracy is often below that of human experts. Here we introduce WHOI-Plankton: a large scale, fine-grained visual recognition dataset for plankton classification, which comprises over 3.4 million expert-labeled images across 70 classes. The labeled image set is complied from over 8 years of near continuous data collection with the IFCB at the Martha's Vineyard Coastal Observatory (MVCO). We discuss relevant metrics for evaluation of classification performance and provide results for a traditional method based on hand-engineered features and two methods based on convolutional neural networks.

Light emission from galaxies exhibit diverse brightness profiles, influenced by factors such as galaxy type, structural features and interactions with other galaxies. Elliptical galaxies feature more uniform light distributions, while spiral and irregular galaxies have complex, varied light profiles due to their structural heterogeneity and star-forming activity. In addition, galaxies with an active galactic nucleus (AGN) feature intense, concentrated emission from gas accretion around supermassive black holes, superimposed on regular galactic light, while quasi-stellar objects (QSO) are the extreme case of the AGN emission dominating the galaxy. The challenge of identifying AGN and QSO has been discussed many times in the literature, often requiring multi-wavelength observations. This paper introduces a novel approach to identify AGN and QSO from a single image. Diffusion models have been recently developed in the machine-learning literature to generate realistic-looking images of everyday objects. Utilising the spatial resolving power of the Euclid VIS images, we created a diffusion model trained on one million sources, without using any source pre-selection or labels. The model learns to reconstruct light distributions of normal galaxies, since the population is dominated by them. We condition the prediction of the central light distribution by masking the central few pixels of each source and reconstruct the light according to the diffusion model. We further use this prediction to identify sources that deviate from this profile by examining the reconstruction error of the few central pixels regenerated in each source's core. Our approach, solely using VIS imaging, features high completeness compared to traditional methods of AGN and QSO selection, including optical, near-infrared, mid-infrared, and X-rays.

Near-field radar imaging systems are recently used in a wide range of applications, such as medical diagnosis, through-wall imaging, concealed weapon detection, and nondestructive evaluation. In this paper, we consider the problem of reconstructing the three-dimensional (3D) complex-valued reflectivity distribution of the near-field scene from sparse multiple-input multiple-output (MIMO) array measurements. Using the alternating direction method of multipliers (ADMM) framework, we solve this inverse problem by enforcing regularization on the magnitude of the complex-valued reflectivity distribution. For this, we provide a general expression for the proximal mapping associated with such regularization functionals. This equivalently corresponds to the solution of a complex-valued denoising problem which involves regularization on the magnitude. By utilizing this expression, we develop a novel and efficient plug-and-play (PnP) reconstruction method that consists of simple update steps. Due to the success of data-adaptive deep priors in various imaging problems, we also train a 3D deep denoiser to exploit within the developed PnP framework for MIMO imaging. The effectiveness of the developed learning-based PnP approach is illustrated under various compressive and noisy observation scenarios using both simulated data and experimental measurements. The performance is also compared with sparsity priors and the commonly used analytical approaches such as back-projection and Kirchhoff migration. The results demonstrate that the developed technique not only provides state-of-the-art reconstruction performance for 3D real-world targets, but also enables fast computation. Our approach provides a unified general framework to effectively handle arbitrary regularization on the magnitude of a complex-valued unknown and is equally applicable to other radar image formation problems (including SAR).

Denoising diffusion models have emerged as the go-to framework for solving inverse problems in imaging. A critical concern regarding these models is their performance on out-of-distribution (OOD) tasks, which remains an under-explored challenge. Realistic reconstructions inconsistent with the measured data can be generated, hallucinating image features that are uniquely present in the training dataset. To simultaneously enforce data-consistency and leverage data-driven priors, we introduce a novel sampling framework called Steerable Conditional Diffusion. This framework adapts the denoising network specifically to the available measured data. Utilising our proposed method, we achieve substantial enhancements in OOD performance across diverse imaging modalities, advancing the robust deployment of denoising diffusion models in real-world applications.

Magnetic Resonance Imaging (MRI) is a critical tool in modern medical diagnostics, yet its prolonged acquisition time remains a critical limitation, especially in time-sensitive clinical scenarios. While undersampling strategies can accelerate image acquisition, they often result in image artifacts and degraded quality. Recent diffusion models have shown promise for reconstructing high-fidelity images from undersampled data by learning powerful image priors; however, most existing approaches either (i) rely on unsupervised score functions without paired supervision or (ii) apply data consistency only as a post-processing step. In this work, we introduce a conditional denoising diffusion framework with iterative data-consistency correction, which differs from prior methods by embedding the measurement model directly into every reverse diffusion step and training the model on paired undersampled-ground truth data. This hybrid design bridges generative flexibility with explicit enforcement of MRI physics. Experiments on the fastMRI dataset demonstrate that our framework consistently outperforms recent state-of-the-art deep learning and diffusion-based methods in SSIM, PSNR, and LPIPS, with LPIPS capturing perceptual improvements more faithfully. These results demonstrate that integrating conditional supervision with iterative consistency updates yields substantial improvements in both pixel-level fidelity and perceptual realism, establishing a principled and practical advance toward robust, accelerated MRI reconstruction.

Blood vessel networks in the brain play a crucial role in stroke research, where understanding their topology is essential for analyzing blood flow dynamics. However, extracting detailed topological vessel network information from microscopy data remains a significant challenge, mainly due to the scarcity of labeled training data and the need for high topological accuracy. This work combines synthetic data generation with deep learning to automatically extract vessel networks as graphs from volumetric microscopy data. To combat data scarcity, we introduce a comprehensive pipeline for generating large-scale synthetic datasets that mirror the characteristics of real vessel networks. Our three-stage approach progresses from abstract graph generation through vessel mask creation to realistic medical image synthesis, incorporating biological constraints and imaging artifacts at each stage. Using this synthetic data, we develop a two-stage deep learning pipeline of 3D U-Net-based models for node detection and edge prediction. Fine-tuning on real microscopy data shows promising adaptation, improving edge prediction F1 scores from 0.496 to 0.626 by training on merely 5 manually labeled samples. These results suggest that automated vessel network extraction is becoming practically feasible, opening new possibilities for large-scale vascular analysis in stroke research.

We present starkiller, an open-source Python package for forward-modeling flux retrieval from integral field unit spectrograph (IFU) datacubes. Starkiller simultaneously provides stellar spectral classification, relative velocity, and line-of-sight extinction for all sources in a catalog, alongside a source-subtracted datacube. It performs synthetic difference imaging by simulating all catalog sources in the field of view, using the catalog for positions and fluxes to scale stellar models, independent of the datacube. This differencing method is particularly powerful for subtracting both point-sources and trailed or even streaked sources from extended astronomical objects. We demonstrate starkiller's effectiveness in improving observations of extended sources in dense stellar fields for VLT/MUSE observations of comets, asteroids and nebulae. We also show that starkiller can treat satellite-impacted VLT/MUSE observations. The package could be applied to tasks as varied as dust extinction in clusters and stellar variability; the stellar modeling using Gaia fluxes is provided as a standalone function. The techniques can be expanded to imagers and to other IFUs.

We propose a novel framework for retinal feature point alignment, designed for learning cross-modality features to enhance matching and registration across multi-modality retinal images. Our model draws on the success of previous learning-based feature detection and description methods. To better leverage unlabeled data and constrain the model to reproduce relevant keypoints, we integrate a keypoint-based segmentation task. It is trained in a self-supervised manner by enforcing segmentation consistency between different augmentations of the same image. By incorporating a keypoint augmented self-supervised layer, we achieve robust feature extraction across modalities. Extensive evaluation on two public datasets and one in-house dataset demonstrates significant improvements in performance for modality-agnostic retinal feature alignment. Our code and model weights are publicly available at https://github.com/MedICL-VU/RetinaIPA.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

Chest X-Ray (CXR) report generation is a promising approach to improving the efficiency of CXR interpretation. However, a significant increase in diagnostic accuracy is required before that can be realised. Motivated by this, we propose a framework that is more inline with a radiologist's workflow by considering longitudinal data. Here, the decoder is additionally conditioned on the report from the subject's previous imaging study via a prompt. We also propose a new reward for reinforcement learning based on CXR-BERT, which computes the similarity between reports. We conduct experiments on the MIMIC-CXR dataset. The results indicate that longitudinal data improves CXR report generation. CXR-BERT is also shown to be a promising alternative to the current state-of-the-art reward based on RadGraph. This investigation indicates that longitudinal CXR report generation can offer a substantial increase in diagnostic accuracy. Our Hugging Face model is available at: https://huggingface.co/aehrc/cxrmate and code is available at: https://github.com/aehrc/cxrmate.

Accelerated magnetic resonance (MR) imaging attempts to reduce acquisition time by collecting data below the Nyquist rate. As an ill-posed inverse problem, many plausible solutions exist, yet the majority of deep learning approaches generate only a single solution. We instead focus on sampling from the posterior distribution, which provides more comprehensive information for downstream inference tasks. To do this, we design a novel conditional normalizing flow (CNF) that infers the signal component in the measurement operator's nullspace, which is later combined with measured data to form complete images. Using fastMRI brain and knee data, we demonstrate fast inference and accuracy that surpasses recent posterior sampling techniques for MRI. Code is available at https://github.com/jwen307/mri_cnf/

Low-light raw denoising is an important and valuable task in computational photography where learning-based methods trained with paired real data are mainstream. However, the limited data volume and complicated noise distribution have constituted a learnability bottleneck for paired real data, which limits the denoising performance of learning-based methods. To address this issue, we present a learnability enhancement strategy to reform paired real data according to noise modeling. Our strategy consists of two efficient techniques: shot noise augmentation (SNA) and dark shading correction (DSC). Through noise model decoupling, SNA improves the precision of data mapping by increasing the data volume and DSC reduces the complexity of data mapping by reducing the noise complexity. Extensive results on the public datasets and real imaging scenarios collectively demonstrate the state-of-the-art performance of our method. Our code is available at: https://github.com/megvii-research/PMN.

Measuring soil health indicators is an important and challenging task that affects farmers' decisions on timing, placement, and quantity of fertilizers applied in the farms. Most existing methods to measure soil health indicators (SHIs) are in-lab wet chemistry or spectroscopy-based methods, which require significant human input and effort, time-consuming, costly, and are low-throughput in nature. To address this challenge, we develop an artificial intelligence (AI)-driven near real-time unmanned aerial vehicle (UAV)-based multispectral sensing (UMS) solution to estimate total nitrogen (TN) of the soil, an important macro-nutrient or SHI that directly affects the crop health. Accurate prediction of soil TN can significantly increase crop yield through informed decision making on the timing of seed planting, and fertilizer quantity and timing. We train two machine learning models including multi-layer perceptron and support vector machine to predict the soil nitrogen using a suite of data classes including multispectral characteristics of the soil and crops in red, near-infrared, and green spectral bands, computed vegetation indices, and environmental variables including air temperature and relative humidity. To generate the ground-truth data or the training data for the machine learning models, we measure the total nitrogen of the soil samples (collected from a farm) using laser-induced breakdown spectroscopy (LIBS).

In the field of medical imaging, the scarcity of large-scale datasets due to privacy restrictions stands as a significant barrier to develop large models for medical. To address this issue, we introduce SynFundus-1M, a high-quality synthetic dataset with over 1 million retinal fundus images and extensive disease and pathologies annotations, which is generated by a Denoising Diffusion Probabilistic Model. The SynFundus-Generator and SynFundus-1M achieve superior Frechet Inception Distance (FID) scores compared to existing methods on main-stream public real datasets. Furthermore, the ophthalmologists evaluation validate the difficulty in discerning these synthetic images from real ones, confirming the SynFundus-1M's authenticity. Through extensive experiments, we demonstrate that both CNN and ViT can benifit from SynFundus-1M by pretraining or training directly. Compared to datasets like ImageNet or EyePACS, models train on SynFundus-1M not only achieve better performance but also faster convergence on various downstream tasks.

Hyperspectral image classification remains a challenging task due to the high dimensionality of spectral data, significant inter-band redundancy, and the limited availability of annotated samples. While recent transformer-based models have improved the global modeling of spectral-spatial dependencies, their scalability and adaptability under label-scarce conditions remain limited. In this work, we propose LoLA-SpecViT(Low-rank adaptation Local Attention Spectral Vision Transformer), a lightweight spectral vision transformer that addresses these limitations through a parameter-efficient architecture tailored to the unique characteristics of hyperspectral imagery. Our model combines a 3D convolutional spectral front-end with local window-based self-attention, enhancing both spectral feature extraction and spatial consistency while reducing computational complexity. To further improve adaptability, we integrate low-rank adaptation (LoRA) into attention and projection layers, enabling fine-tuning with over 80\% fewer trainable parameters. A novel cyclical learning rate scheduler modulates LoRA adaptation strength during training, improving convergence and generalisation. Extensive experiments on three benchmark datasets WHU-Hi LongKou, WHU-Hi HongHu, and Salinas demonstrate that LoLA-SpecViT consistently outperforms state-of-the-art baselines, achieving up to 99.91\% accuracy with substantially fewer parameters and enhanced robustness under low-label regimes. The proposed framework provides a scalable and generalizable solution for real-world HSI applications in agriculture, environmental monitoring, and remote sensing analytics. Our code is available in the following https://github.com/FadiZidiDz/LoLA-SpecViT{GitHub Repository}.

Detecting breast cancer early is of the utmost importance to effectively treat the millions of women afflicted by breast cancer worldwide every year. Although mammography is the primary imaging modality for screening breast cancer, there is an increasing interest in adding magnetic resonance imaging (MRI) to screening programmes, particularly for women at high risk. Recent guidelines by the European Society of Breast Imaging (EUSOBI) recommended breast MRI as a supplemental screening tool for women with dense breast tissue. However, acquiring and reading MRI scans requires significantly more time from expert radiologists. This highlights the need to develop new automated methods to detect cancer accurately using MRI and Artificial Intelligence (AI), which have the potential to support radiologists in breast MRI interpretation and classification and help detect cancer earlier. For this reason, the ODELIA consortium has made this multi-centre dataset publicly available to assist in developing AI tools for the detection of breast cancer on MRI.

Recent advancements in medical imaging and artificial intelligence (AI) have greatly enhanced diagnostic capabilities, but the development of effective deep learning (DL) models is still constrained by the lack of high-quality annotated datasets. The traditional manual annotation process by medical experts is time- and resource-intensive, limiting the scalability of these datasets. In this work, we introduce a robust and versatile framework that combines AI and crowdsourcing to improve both the quality and quantity of medical image datasets across different modalities. Our approach utilises a user-friendly online platform that enables a diverse group of crowd annotators to label medical images efficiently. By integrating the MedSAM segmentation AI with this platform, we accelerate the annotation process while maintaining expert-level quality through an algorithm that merges crowd-labelled images. Additionally, we employ pix2pixGAN, a generative AI model, to expand the training dataset with synthetic images that capture realistic morphological features. These methods are combined into a cohesive framework designed to produce an enhanced dataset, which can serve as a universal pre-processing pipeline to boost the training of any medical deep learning segmentation model. Our results demonstrate that this framework significantly improves model performance, especially when training data is limited.

Availability of large and diverse medical datasets is often challenged by privacy and data sharing restrictions. For successful application of machine learning techniques for disease diagnosis, prognosis, and precision medicine, large amounts of data are necessary for model building and optimization. To help overcome such limitations in the context of brain MRI, we present NeuroSynth: a collection of generative models of normative regional volumetric features derived from structural brain imaging. NeuroSynth models are trained on real brain imaging regional volumetric measures from the iSTAGING consortium, which encompasses over 40,000 MRI scans across 13 studies, incorporating covariates such as age, sex, and race. Leveraging NeuroSynth, we produce and offer 18,000 synthetic samples spanning the adult lifespan (ages 22-90 years), alongside the model's capability to generate unlimited data. Experimental results indicate that samples generated from NeuroSynth agree with the distributions obtained from real data. Most importantly, the generated normative data significantly enhance the accuracy of downstream machine learning models on tasks such as disease classification. Data and models are available at: https://huggingface.co/spaces/rongguangw/neuro-synth.

Optical coherence tomography (OCT) is a non-invasive imaging technique with extensive clinical applications in ophthalmology. OCT enables the visualization of the retinal layers, playing a vital role in the early detection and monitoring of retinal diseases. OCT uses the principle of light wave interference to create detailed images of the retinal microstructures, making it a valuable tool for diagnosing ocular conditions. This work presents an open-access OCT dataset (OCTDL) comprising over 1600 high-resolution OCT images labeled according to disease group and retinal pathology. The dataset consists of OCT records of patients with Age-related Macular Degeneration (AMD), Diabetic Macular Edema (DME), Epiretinal Membrane (ERM), Retinal Artery Occlusion (RAO), Retinal Vein Occlusion (RVO), and Vitreomacular Interface Disease (VID). The images were acquired with an Optovue Avanti RTVue XR using raster scanning protocols with dynamic scan length and image resolution. Each retinal b-scan was acquired by centering on the fovea and interpreted and cataloged by an experienced retinal specialist. In this work, we applied Deep Learning classification techniques to this new open-access dataset.

Concerns about the reproducibility of deep learning research are more prominent than ever, with no clear solution in sight. The relevance of machine learning research can only be improved if we also employ empirical rigor that incorporates reproducibility guidelines, especially so in the medical imaging field. The Medical Imaging with Deep Learning (MIDL) conference has made advancements in this direction by advocating open access, and recently also recommending authors to make their code public - both aspects being adopted by the majority of the conference submissions. This helps the reproducibility of the methods, however, there is currently little or no support for further evaluation of these supplementary material, making them vulnerable to poor quality, which affects the impact of the entire submission. We have evaluated all accepted full paper submissions to MIDL between 2018 and 2022 using established, but slightly adjusted guidelines on reproducibility and the quality of the public repositories. The evaluations show that publishing repositories and using public datasets are becoming more popular, which helps traceability, but the quality of the repositories has not improved over the years, leaving room for improvement in every aspect of designing repositories. Merely 22% of all submissions contain a repository that were deemed repeatable using our evaluations. From the commonly encountered issues during the evaluations, we propose a set of guidelines for machine learning-related research for medical imaging applications, adjusted specifically for future submissions to MIDL.

Optical coherence tomography angiography (OCTA) is a novel imaging modality that has been widely utilized in ophthalmology and neuroscience studies to observe retinal vessels and microvascular systems. However, publicly available OCTA datasets remain scarce. In this paper, we introduce the largest and most comprehensive OCTA dataset dubbed OCTA-500, which contains OCTA imaging under two fields of view (FOVs) from 500 subjects. The dataset provides rich images and annotations including two modalities (OCT/OCTA volumes), six types of projections, four types of text labels (age / gender / eye / disease) and seven types of segmentation labels (large vessel/capillary/artery/vein/2D FAZ/3D FAZ/retinal layers). Then, we propose a multi-object segmentation task called CAVF, which integrates capillary segmentation, artery segmentation, vein segmentation, and FAZ segmentation under a unified framework. In addition, we optimize the 3D-to-2D image projection network (IPN) to IPN-V2 to serve as one of the segmentation baselines. Experimental results demonstrate that IPN-V2 achieves an ~10% mIoU improvement over IPN on CAVF task. Finally, we further study the impact of several dataset characteristics: the training set size, the model input (OCT/OCTA, 3D volume/2D projection), the baseline networks, and the diseases. The dataset and code are publicly available at: https://ieee-dataport.org/open-access/octa-500.

Optical coherence tomography (OCT) is a non-invasive imaging modality which is widely used in clinical ophthalmology. OCT images are capable of visualizing deep retinal layers which is crucial for early diagnosis of retinal diseases. In this paper, we describe a comprehensive open-access database containing more than 500 highresolution images categorized into different pathological conditions. The image classes include Normal (NO), Macular Hole (MH), Age-related Macular Degeneration (AMD), Central Serous Retinopathy (CSR), and Diabetic Retinopathy (DR). The images were obtained from a raster scan protocol with a 2mm scan length and 512x1024 pixel resolution. We have also included 25 normal OCT images with their corresponding ground truth delineations which can be used for an accurate evaluation of OCT image segmentation. In addition, we have provided a user-friendly GUI which can be used by clinicians for manual (and semi-automated) segmentation.

Foundational mapping remains a challenge in many parts of the world, particularly in dynamic scenarios such as natural disasters when timely updates are critical. Updating maps is currently a highly manual process requiring a large number of human labelers to either create features or rigorously validate automated outputs. We propose that the frequent revisits of earth imaging satellite constellations may accelerate existing efforts to quickly update foundational maps when combined with advanced machine learning techniques. Accordingly, the SpaceNet partners (CosmiQ Works, Radiant Solutions, and NVIDIA), released a large corpus of labeled satellite imagery on Amazon Web Services (AWS) called SpaceNet. The SpaceNet partners also launched a series of public prize competitions to encourage improvement of remote sensing machine learning algorithms. The first two of these competitions focused on automated building footprint extraction, and the most recent challenge focused on road network extraction. In this paper we discuss the SpaceNet imagery, labels, evaluation metrics, prize challenge results to date, and future plans for the SpaceNet challenge series.

Multi-modal data abounds in biomedicine, such as radiology images and reports. Interpreting this data at scale is essential for improving clinical care and accelerating clinical research. Biomedical text with its complex semantics poses additional challenges in vision--language modelling compared to the general domain, and previous work has used insufficiently adapted models that lack domain-specific language understanding. In this paper, we show that principled textual semantic modelling can substantially improve contrastive learning in self-supervised vision--language processing. We release a language model that achieves state-of-the-art results in radiology natural language inference through its improved vocabulary and novel language pretraining objective leveraging semantics and discourse characteristics in radiology reports. Further, we propose a self-supervised joint vision--language approach with a focus on better text modelling. It establishes new state of the art results on a wide range of publicly available benchmarks, in part by leveraging our new domain-specific language model. We release a new dataset with locally-aligned phrase grounding annotations by radiologists to facilitate the study of complex semantic modelling in biomedical vision--language processing. A broad evaluation, including on this new dataset, shows that our contrastive learning approach, aided by textual-semantic modelling, outperforms prior methods in segmentation tasks, despite only using a global-alignment objective.

Vision-Language Models (VLMs) trained via contrastive learning have achieved notable success in natural image tasks. However, their application in the medical domain remains limited due to the scarcity of openly accessible, large-scale medical image-text datasets. Existing medical VLMs either train on closed-source proprietary or relatively small open-source datasets that do not generalize well. Similarly, most models remain specific to a single or limited number of medical imaging domains, again restricting their applicability to other modalities. To address this gap, we introduce UniMed, a large-scale, open-source multi-modal medical dataset comprising over 5.3 million image-text pairs across six diverse imaging modalities: X-ray, CT, MRI, Ultrasound, Pathology, and Fundus. UniMed is developed using a data-collection framework that leverages Large Language Models (LLMs) to transform modality-specific classification datasets into image-text formats while incorporating existing image-text data from the medical domain, facilitating scalable VLM pretraining. Using UniMed, we trained UniMed-CLIP, a unified VLM for six modalities that significantly outperforms existing generalist VLMs and matches modality-specific medical VLMs, achieving notable gains in zero-shot evaluations. For instance, UniMed-CLIP improves over BiomedCLIP (trained on proprietary data) by an absolute gain of +12.61, averaged over 21 datasets, while using 3x less training data. To facilitate future research, we release UniMed dataset, training codes, and models at https://github.com/mbzuai-oryx/UniMed-CLIP.

Segmenting stroke lesions in Magnetic Resonance Imaging (MRI) is challenging due to diverse clinical imaging domains, with existing models struggling to generalise across different MRI acquisition parameters and sequences. In this work, we propose two novel physics-constrained approaches using synthetic quantitative MRI (qMRI) images to enhance the robustness and generalisability of segmentation models. We trained a qMRI estimation model to predict qMRI maps from MPRAGE images, which were used to simulate diverse MRI sequences for segmentation training. A second approach built upon prior work in synthetic data for stroke lesion segmentation, generating qMRI maps from a dataset of tissue labels. The proposed approaches improved over the baseline nnUNet on a variety of out-of-distribution datasets, with the second approach outperforming the prior synthetic data method.

Neural Radiance Fields (NeRFs) quickly evolved as the new de-facto standard for the task of novel view synthesis when trained on a set of RGB images. In this paper, we conduct a comprehensive evaluation of neural scene representations, such as NeRFs, in the context of multi-modal learning. Specifically, we present four different strategies of how to incorporate a second modality, other than RGB, into NeRFs: (1) training from scratch independently on both modalities; (2) pre-training on RGB and fine-tuning on the second modality; (3) adding a second branch; and (4) adding a separate component to predict (color) values of the additional modality. We chose thermal imaging as second modality since it strongly differs from RGB in terms of radiosity, making it challenging to integrate into neural scene representations. For the evaluation of the proposed strategies, we captured a new publicly available multi-view dataset, ThermalMix, consisting of six common objects and about 360 RGB and thermal images in total. We employ cross-modality calibration prior to data capturing, leading to high-quality alignments between RGB and thermal images. Our findings reveal that adding a second branch to NeRF performs best for novel view synthesis on thermal images while also yielding compelling results on RGB. Finally, we also show that our analysis generalizes to other modalities, including near-infrared images and depth maps. Project page: https://mert-o.github.io/ThermalNeRF/.

Diffusion Magnetic Resonance Imaging (dMRI) plays a crucial role in the noninvasive investigation of tissue microstructural properties and structural connectivity in the in vivo human brain. However, to effectively capture the intricate characteristics of water diffusion at various directions and scales, it is important to employ comprehensive q-space sampling. Unfortunately, this requirement leads to long scan times, limiting the clinical applicability of dMRI. To address this challenge, we propose SSOR, a Simultaneous q-Space sampling Optimization and Reconstruction framework. We jointly optimize a subset of q-space samples using a continuous representation of spherical harmonic functions and a reconstruction network. Additionally, we integrate the unique properties of diffusion magnetic resonance imaging (dMRI) in both the q-space and image domains by applying l1-norm and total-variation regularization. The experiments conducted on HCP data demonstrate that SSOR has promising strengths both quantitatively and qualitatively and exhibits robustness to noise.

Ultrasound Localization Microscopy (ULM) enables imaging of vascular structures in the micrometer range by accumulating contrast agent particle locations over time. Precise and efficient target localization accuracy remains an active research topic in the ULM field to further push the boundaries of this promising medical imaging technology. Existing work incorporates Delay-And-Sum (DAS) beamforming into particle localization pipelines, which ultimately determines the ULM image resolution capability. In this paper we propose to feed unprocessed Radio-Frequency (RF) data into a super-resolution network while bypassing DAS beamforming and its limitations. To facilitate this, we demonstrate label projection and inverse point transformation between B-mode and RF coordinate space as required by our approach. We assess our method against state-of-the-art techniques based on a public dataset featuring in silico and in vivo data. Results from our RF-trained network suggest that excluding DAS beamforming offers a great potential to optimize on the ULM resolution performance.

Recent advances in generative AI have brought incredible breakthroughs in several areas, including medical imaging. These generative models have tremendous potential not only to help safely share medical data via synthetic datasets but also to perform an array of diverse applications, such as anomaly detection, image-to-image translation, denoising, and MRI reconstruction. However, due to the complexity of these models, their implementation and reproducibility can be difficult. This complexity can hinder progress, act as a use barrier, and dissuade the comparison of new methods with existing works. In this study, we present MONAI Generative Models, a freely available open-source platform that allows researchers and developers to easily train, evaluate, and deploy generative models and related applications. Our platform reproduces state-of-art studies in a standardised way involving different architectures (such as diffusion models, autoregressive transformers, and GANs), and provides pre-trained models for the community. We have implemented these models in a generalisable fashion, illustrating that their results can be extended to 2D or 3D scenarios, including medical images with different modalities (like CT, MRI, and X-Ray data) and from different anatomical areas. Finally, we adopt a modular and extensible approach, ensuring long-term maintainability and the extension of current applications for future features.

With society's increasing reliance on digital data sharing, the protection of sensitive information has become critical. Encryption serves as one of the privacy-preserving methods; however, its realization in the audio domain predominantly relies on signal processing or software methods embedded into hardware. In this paper, we introduce LenslessMic, a hybrid optical hardware-based encryption method that utilizes a lensless camera as a physical layer of security applicable to multiple types of audio. We show that LenslessMic enables (1) robust authentication of audio recordings and (2) encryption strength that can rival the search space of 256-bit digital standards, while maintaining high-quality signals and minimal loss of content information. The approach is validated with a low-cost Raspberry Pi prototype and is open-sourced together with datasets to facilitate research in the area.

Vision-and-language models (VLMs) have been increasingly explored in the medical domain, particularly following the success of CLIP in general domain. However, unlike the relatively straightforward pairing of 2D images and text, curating large-scale paired data in the medical field for volumetric modalities such as CT scans remains a challenging and time-intensive process. This difficulty often limits the performance on downstream tasks. To address these challenges, we propose a novel vision-language pre-training (VLP) framework, termed as VELVET-Med, specifically designed for limited volumetric data such as 3D CT and associated radiology reports. Instead of relying on large-scale data collection, our method focuses on the development of effective pre-training objectives and model architectures. The key contributions are: 1) We incorporate uni-modal self-supervised learning into VLP framework, which are often underexplored in the existing literature. 2) We propose a novel language encoder, termed as TriBERT, for learning multi-level textual semantics. 3) We devise the hierarchical contrastive learning to capture multi-level vision-language correspondence. Using only 38,875 scan-report pairs, our approach seeks to uncover rich spatial and semantic relationships embedded in volumetric medical images and corresponding clinical narratives, thereby enhancing the generalization ability of the learned encoders. The resulting encoders exhibit strong transferability, achieving state-of-the-art performance across a wide range of downstream tasks, including 3D segmentation, cross-modal retrieval, visual question answering, and report generation.

Geospatial raster data, such as that collected by satellite-based imaging systems at different times and spectral bands, hold immense potential for enabling a wide range of high-impact applications. This potential stems from the rich information that is spatially and temporally contextualized across multiple channels and sensing modalities. Recent work has adapted existing self-supervised learning approaches for such geospatial data. However, they fall short of scalable model architectures, leading to inflexibility and computational inefficiencies when faced with an increasing number of channels and modalities. To address these limitations, we introduce Low-rank Efficient Spatial-Spectral Vision Transformer with three key innovations: i) the LESS Attention Block that approximates high-dimensional spatial-spectral attention through Kronecker's product of the low-dimensional spatial and spectral attention components; ii) the Continuous Positional-Channel Embedding Layer that preserves both the continuity and physical characteristics of each spatial-spectral patch; and iii) the Perception Field Mask that exploits local spatial dependencies by constraining attention to neighboring patches. To evaluate the proposed innovations, we construct GFM-Bench, which serves as a comprehensive benchmark for such geospatial raster data. We pretrain LESS ViT using a Hyperspectral Masked Autoencoder framework with integrated positional and channel masking strategies. Experimental results demonstrate that our proposed method achieves competitive performance against state-of-the-art multi-modal geospatial foundation models while outperforming them on cross-satellite generalization tasks with higher computational efficiency. The flexibility and extensibility of our framework make it a promising direction for future geospatial data analysis tasks that involve a wide range of modalities and channels.

We demonstrate a compact, cost-effective snapshot spectral imaging system named Aperture Diffraction Imaging Spectrometer (ADIS), which consists only of an imaging lens with an ultra-thin orthogonal aperture mask and a mosaic filter sensor, requiring no additional physical footprint compared to common RGB cameras. Then we introduce a new optical design that each point in the object space is multiplexed to discrete encoding locations on the mosaic filter sensor by diffraction-based spatial-spectral projection engineering generated from the orthogonal mask. The orthogonal projection is uniformly accepted to obtain a weakly calibration-dependent data form to enhance modulation robustness. Meanwhile, the Cascade Shift-Shuffle Spectral Transformer (CSST) with strong perception of the diffraction degeneration is designed to solve a sparsity-constrained inverse problem, realizing the volume reconstruction from 2D measurements with Large amount of aliasing. Our system is evaluated by elaborating the imaging optical theory and reconstruction algorithm with demonstrating the experimental imaging under a single exposure. Ultimately, we achieve the sub-super-pixel spatial resolution and high spectral resolution imaging. The code will be available at: https://github.com/Krito-ex/CSST.

While deep learning technologies are now capable of generating realistic images confusing humans, the research efforts are turning to the synthesis of images for more concrete and application-specific purposes. Facial image generation based on vocal characteristics from speech is one of such important yet challenging tasks. It is the key enabler to influential use cases of image generation, especially for business in public security and entertainment. Existing solutions to the problem of speech2face renders limited image quality and fails to preserve facial similarity due to the lack of quality dataset for training and appropriate integration of vocal features. In this paper, we investigate these key technical challenges and propose Speech Fusion to Face, or SF2F in short, attempting to address the issue of facial image quality and the poor connection between vocal feature domain and modern image generation models. By adopting new strategies on data model and training, we demonstrate dramatic performance boost over state-of-the-art solution, by doubling the recall of individual identity, and lifting the quality score from 15 to 19 based on the mutual information score with VGGFace classifier.

Medical image segmentation is crucial for many healthcare tasks, including disease diagnosis and treatment planning. One key area is the segmentation of skin lesions, which is vital for diagnosing skin cancer and monitoring patients. In this context, this paper introduces SegDT, a new segmentation model based on diffusion transformer (DiT). SegDT is designed to work on low-cost hardware and incorporates Rectified Flow, which improves the generation quality at reduced inference steps and maintains the flexibility of standard diffusion models. Our method is evaluated on three benchmarking datasets and compared against several existing works, achieving state-of-the-art results while maintaining fast inference speeds. This makes the proposed model appealing for real-world medical applications. This work advances the performance and capabilities of deep learning models in medical image analysis, enabling faster, more accurate diagnostic tools for healthcare professionals. The code is made publicly available at https://github.com/Bekhouche/SegDT{GitHub}.

Despite considerable progress in stereo depth estimation, omnidirectional imaging remains underexplored, mainly due to the lack of appropriate data. We introduce Helvipad, a real-world dataset for omnidirectional stereo depth estimation, consisting of 40K frames from video sequences across diverse environments, including crowded indoor and outdoor scenes with diverse lighting conditions. Collected using two 360{\deg} cameras in a top-bottom setup and a LiDAR sensor, the dataset includes accurate depth and disparity labels by projecting 3D point clouds onto equirectangular images. Additionally, we provide an augmented training set with a significantly increased label density by using depth completion. We benchmark leading stereo depth estimation models for both standard and omnidirectional images. The results show that while recent stereo methods perform decently, a significant challenge persists in accurately estimating depth in omnidirectional imaging. To address this, we introduce necessary adaptations to stereo models, achieving improved performance.

Large vision-language models (VLMs) have made great achievements in Earth vision. However, complex disaster scenes with diverse disaster types, geographic regions, and satellite sensors have posed new challenges for VLM applications. To fill this gap, we curate a remote sensing vision-language dataset (DisasterM3) for global-scale disaster assessment and response. DisasterM3 includes 26,988 bi-temporal satellite images and 123k instruction pairs across 5 continents, with three characteristics: 1) Multi-hazard: DisasterM3 involves 36 historical disaster events with significant impacts, which are categorized into 10 common natural and man-made disasters. 2)Multi-sensor: Extreme weather during disasters often hinders optical sensor imaging, making it necessary to combine Synthetic Aperture Radar (SAR) imagery for post-disaster scenes. 3) Multi-task: Based on real-world scenarios, DisasterM3 includes 9 disaster-related visual perception and reasoning tasks, harnessing the full potential of VLM's reasoning ability with progressing from disaster-bearing body recognition to structural damage assessment and object relational reasoning, culminating in the generation of long-form disaster reports. We extensively evaluated 14 generic and remote sensing VLMs on our benchmark, revealing that state-of-the-art models struggle with the disaster tasks, largely due to the lack of a disaster-specific corpus, cross-sensor gap, and damage object counting insensitivity. Focusing on these issues, we fine-tune four VLMs using our dataset and achieve stable improvements across all tasks, with robust cross-sensor and cross-disaster generalization capabilities.

Medical Visual Language Models have shown great potential in various healthcare applications, including medical image captioning and diagnostic assistance. However, most existing models rely on text-based instructions, limiting their usability in real-world clinical environments especially in scenarios such as surgery, text-based interaction is often impractical for physicians. In addition, current medical image analysis models typically lack comprehensive reasoning behind their predictions, which reduces their reliability for clinical decision-making. Given that medical diagnosis errors can have life-changing consequences, there is a critical need for interpretable and rational medical assistance. To address these challenges, we introduce an end-to-end speech-driven medical VLM, SilVar-Med, a multimodal medical image assistant that integrates speech interaction with VLMs, pioneering the task of voice-based communication for medical image analysis. In addition, we focus on the interpretation of the reasoning behind each prediction of medical abnormalities with a proposed reasoning dataset. Through extensive experiments, we demonstrate a proof-of-concept study for reasoning-driven medical image interpretation with end-to-end speech interaction. We believe this work will advance the field of medical AI by fostering more transparent, interactive, and clinically viable diagnostic support systems. Our code and dataset are publicly available at SiVar-Med.

The rapid advancement of deep learning has intensified the need for comprehensive data for use by autonomous driving algorithms. High-quality datasets are crucial for the development of effective data-driven autonomous driving solutions. Next-generation autonomous driving datasets must be multimodal, incorporating data from advanced sensors that feature extensive data coverage, detailed annotations, and diverse scene representation. To address this need, we present OmniHD-Scenes, a large-scale multimodal dataset that provides comprehensive omnidirectional high-definition data. The OmniHD-Scenes dataset combines data from 128-beam LiDAR, six cameras, and six 4D imaging radar systems to achieve full environmental perception. The dataset comprises 1501 clips, each approximately 30-s long, totaling more than 450K synchronized frames and more than 5.85 million synchronized sensor data points. We also propose a novel 4D annotation pipeline. To date, we have annotated 200 clips with more than 514K precise 3D bounding boxes. These clips also include semantic segmentation annotations for static scene elements. Additionally, we introduce a novel automated pipeline for generation of the dense occupancy ground truth, which effectively leverages information from non-key frames. Alongside the proposed dataset, we establish comprehensive evaluation metrics, baseline models, and benchmarks for 3D detection and semantic occupancy prediction. These benchmarks utilize surround-view cameras and 4D imaging radar to explore cost-effective sensor solutions for autonomous driving applications. Extensive experiments demonstrate the effectiveness of our low-cost sensor configuration and its robustness under adverse conditions. Data will be released at https://www.2077ai.com/OmniHD-Scenes.

AI is revolutionizing MRI along the acquisition and processing chain. Advanced AI frameworks have been developed to apply AI in various successive tasks, such as image reconstruction, quantitative parameter map estimation, and image segmentation. Existing frameworks are often designed to perform tasks independently or are focused on specific models or datasets, limiting generalization. We introduce ATOMMIC, an open-source toolbox that streamlines AI applications for accelerated MRI reconstruction and analysis. ATOMMIC implements several tasks using DL networks and enables MultiTask Learning (MTL) to perform related tasks integrated, targeting generalization in the MRI domain. We first review the current state of AI frameworks for MRI through a comprehensive literature search and by parsing 12,479 GitHub repositories. We benchmark 25 DL models on eight publicly available datasets to present distinct applications of ATOMMIC on accelerated MRI reconstruction, image segmentation, quantitative parameter map estimation, and joint accelerated MRI reconstruction and image segmentation utilizing MTL. Our findings demonstrate that ATOMMIC is the only MTL framework with harmonized complex-valued and real-valued data support. Evaluations on single tasks show that physics-based models, which enforce data consistency by leveraging the physical properties of MRI, outperform other models in reconstructing highly accelerated acquisitions. Physics-based models that produce high reconstruction quality can accurately estimate quantitative parameter maps. When high-performing reconstruction models are combined with robust segmentation networks utilizing MTL, performance is improved in both tasks. ATOMMIC facilitates MRI reconstruction and analysis by standardizing workflows, enhancing data interoperability, integrating unique features like MTL, and effectively benchmarking DL models.

Near-field multiple-input multiple-output (MIMO) radar imaging systems have recently gained significant attention. In this paper, we develop novel non-iterative deep learning-based reconstruction methods for real-time near-field MIMO imaging. The goal is to achieve high image quality with low computational cost at compressive settings. The developed approaches have two stages. In the first approach, physics-based initial stage performs adjoint operation to back-project the measurements to the image-space, and deep neural network (DNN)-based second stage converts the 3D backprojected measurements to a magnitude-only reflectivity image. Since scene reflectivities often have random phase, DNN processes directly the magnitude of the adjoint result. As DNN, 3D U-Net is used to jointly exploit range and cross-range correlations. To comparatively evaluate the significance of exploiting physics in a learning-based approach, two additional approaches that replace the physics-based first stage with fully connected layers are also developed as purely learning-based methods. The performance is also analyzed by changing the DNN architecture for the second stage to include complex-valued processing (instead of magnitude-only processing), 2D convolution kernels (instead of 3D), and ResNet architecture (instead of U-Net). Moreover, we develop a synthesizer to generate large-scale dataset for training with 3D extended targets. We illustrate the performance through experimental data and extensive simulations. The results show the effectiveness of the developed physics-based learned reconstruction approach in terms of both run-time and image quality at highly compressive settings. Our source codes and dataset are made available at GitHub.

Reliable medical image classification requires accurate predictions and well-calibrated uncertainty estimates, especially in high-stakes clinical settings. This work presents MedSymmFlow, a generative-discriminative hybrid model built on Symmetrical Flow Matching, designed to unify classification, generation, and uncertainty quantification in medical imaging. MedSymmFlow leverages a latent-space formulation that scales to high-resolution inputs and introduces a semantic mask conditioning mechanism to enhance diagnostic relevance. Unlike standard discriminative models, it naturally estimates uncertainty through its generative sampling process. The model is evaluated on four MedMNIST datasets, covering a range of modalities and pathologies. The results show that MedSymmFlow matches or exceeds the performance of established baselines in classification accuracy and AUC, while also delivering reliable uncertainty estimates validated by performance improvements under selective prediction.

Endorectal ultrasound (ERUS) is an important imaging modality that provides high reliability for diagnosing the depth and boundary of invasion in colorectal cancer. However, the lack of a large-scale ERUS dataset with high-quality annotations hinders the development of automatic ultrasound diagnostics. In this paper, we collected and annotated the first benchmark dataset that covers diverse ERUS scenarios, i.e. colorectal cancer segmentation, detection, and infiltration depth staging. Our ERUS-10K dataset comprises 77 videos and 10,000 high-resolution annotated frames. Based on this dataset, we further introduce a benchmark model for colorectal cancer segmentation, named the Adaptive Sparse-context TRansformer (ASTR). ASTR is designed based on three considerations: scanning mode discrepancy, temporal information, and low computational complexity. For generalizing to different scanning modes, the adaptive scanning-mode augmentation is proposed to convert between raw sector images and linear scan ones. For mining temporal information, the sparse-context transformer is incorporated to integrate inter-frame local and global features. For reducing computational complexity, the sparse-context block is introduced to extract contextual features from auxiliary frames. Finally, on the benchmark dataset, the proposed ASTR model achieves a 77.6% Dice score in rectal cancer segmentation, largely outperforming previous state-of-the-art methods.

Methane emissions from livestock, particularly cattle, significantly contribute to climate change. Effective methane emission mitigation strategies are crucial as the global population and demand for livestock products increase. We introduce Gasformer, a novel semantic segmentation architecture for detecting low-flow rate methane emissions from livestock, and controlled release experiments using optical gas imaging. We present two unique datasets captured with a FLIR GF77 OGI camera. Gasformer leverages a Mix Vision Transformer encoder and a Light-Ham decoder to generate multi-scale features and refine segmentation maps. Gasformer outperforms other state-of-the-art models on both datasets, demonstrating its effectiveness in detecting and segmenting methane plumes in controlled and real-world scenarios. On the livestock dataset, Gasformer achieves mIoU of 88.56%, surpassing other state-of-the-art models. Materials are available at: github.com/toqitahamid/Gasformer.

Coronary artery disease (CAD) remains the leading cause of death globally and invasive coronary angiography (ICA) is considered the gold standard of anatomical imaging evaluation when CAD is suspected. However, risk evaluation based on ICA has several limitations, such as visual assessment of stenosis severity, which has significant interobserver variability. This motivates to development of a lesion classification system that can support specialists in their clinical procedures. Although deep learning classification methods are well-developed in other areas of medical imaging, ICA image classification is still at an early stage. One of the most important reasons is the lack of available and high-quality open-access datasets. In this paper, we reported a new annotated ICA images dataset, CADICA, to provide the research community with a comprehensive and rigorous dataset of coronary angiography consisting of a set of acquired patient videos and associated disease-related metadata. This dataset can be used by clinicians to train their skills in angiographic assessment of CAD severity and by computer scientists to create computer-aided diagnostic systems to help in such assessment. In addition, baseline classification methods are proposed and analyzed, validating the functionality of CADICA and giving the scientific community a starting point to improve CAD detection.

Inpainting has recently been proposed as a successful deep learning technique for unsupervised medical image model discovery. The masks used for inpainting are generally independent of the dataset and are not tailored to perform on different given classes of anatomy. In this work, we introduce a method for generating shape-aware masks for inpainting, which aims at learning the statistical shape prior. We hypothesize that although the variation of masks improves the generalizability of inpainting models, the shape of the masks should follow the topology of the organs of interest. Hence, we propose an unsupervised guided masking approach based on an off-the-shelf inpainting model and a superpixel over-segmentation algorithm to generate a wide range of shape-dependent masks. Experimental results on abdominal MR image reconstruction show the superiority of our proposed masking method over standard methods using square-shaped or dataset of irregular shape masks.

Merging multi-exposure images is a common approach for obtaining high dynamic range (HDR) images, with the primary challenge being the avoidance of ghosting artifacts in dynamic scenes. Recent methods have proposed using deep neural networks for deghosting. However, the methods typically rely on sufficient data with HDR ground-truths, which are difficult and costly to collect. In this work, to eliminate the need for labeled data, we propose SelfHDR, a self-supervised HDR reconstruction method that only requires dynamic multi-exposure images during training. Specifically, SelfHDR learns a reconstruction network under the supervision of two complementary components, which can be constructed from multi-exposure images and focus on HDR color as well as structure, respectively. The color component is estimated from aligned multi-exposure images, while the structure one is generated through a structure-focused network that is supervised by the color component and an input reference (\eg, medium-exposure) image. During testing, the learned reconstruction network is directly deployed to predict an HDR image. Experiments on real-world images demonstrate our SelfHDR achieves superior results against the state-of-the-art self-supervised methods, and comparable performance to supervised ones. Codes are available at https://github.com/cszhilu1998/SelfHDR

Vision-Language Pre-training (VLP) is drawing increasing interest for its ability to minimize manual annotation requirements while enhancing semantic understanding in downstream tasks. However, its reliance on image-text datasets poses challenges due to privacy concerns and the high cost of obtaining paired annotations. Data augmentation emerges as a viable strategy to address this issue, yet existing methods often fall short of capturing the subtle and complex variations in medical data due to limited diversity. To this end, we propose MedCutMix, a novel multi-modal disease-centric data augmentation method. MedCutMix performs diagnostic sentence CutMix within medical reports and establishes the cross-attention between the diagnostic sentence and medical image to guide attentive manifold mix within the imaging modality. Our approach surpasses previous methods across four downstream radiology diagnosis datasets, highlighting its effectiveness in enhancing performance and generalizability in radiology VLP.

In the era of information explosion, efficiently leveraging large-scale unlabeled data while minimizing the reliance on high-quality pixel-level annotations remains a critical challenge in the field of medical imaging. Semi-supervised learning (SSL) enhances the utilization of unlabeled data by facilitating knowledge transfer, significantly improving the performance of fully supervised models and emerging as a highly promising research direction in medical image analysis. Inspired by the ability of Vision Foundation Models (e.g., SAM-2) to provide rich prior knowledge, we propose SSS (Semi-Supervised SAM-2), a novel approach that leverages SAM-2's robust feature extraction capabilities to uncover latent knowledge in unlabeled medical images, thus effectively enhancing feature support for fully supervised medical image segmentation. Specifically, building upon the single-stream "weak-to-strong" consistency regularization framework, this paper introduces a Discriminative Feature Enhancement (DFE) mechanism to further explore the feature discrepancies introduced by various data augmentation strategies across multiple views. By leveraging feature similarity and dissimilarity across multi-scale augmentation techniques, the method reconstructs and models the features, thereby effectively optimizing the salient regions. Furthermore, a prompt generator is developed that integrates Physical Constraints with a Sliding Window (PCSW) mechanism to generate input prompts for unlabeled data, fulfilling SAM-2's requirement for additional prompts. Extensive experiments demonstrate the superiority of the proposed method for semi-supervised medical image segmentation on two multi-label datasets, i.e., ACDC and BHSD. Notably, SSS achieves an average Dice score of 53.15 on BHSD, surpassing the previous state-of-the-art method by +3.65 Dice. Code will be available at https://github.com/AIGeeksGroup/SSS.

Agentic systems built on large language models (LLMs) offer promising capabilities for automating complex workflows in healthcare AI. We introduce mAIstro, an open-source, autonomous multi-agentic framework for end-to-end development and deployment of medical AI models. The system orchestrates exploratory data analysis, radiomic feature extraction, image segmentation, classification, and regression through a natural language interface, requiring no coding from the user. Built on a modular architecture, mAIstro supports both open- and closed-source LLMs, and was evaluated using a large and diverse set of prompts across 16 open-source datasets, covering a wide range of imaging modalities, anatomical regions, and data types. The agents successfully executed all tasks, producing interpretable outputs and validated models. This work presents the first agentic framework capable of unifying data analysis, AI model development, and inference across varied healthcare applications, offering a reproducible and extensible foundation for clinical and research AI integration. The code is available at: https://github.com/eltzanis/mAIstro

Whole-heart segmentation from CT and MRI scans is crucial for cardiovascular disease analysis, yet existing methods struggle with modality-specific biases and the need for extensive labeled datasets. To address these challenges, we propose a foundation model for whole-heart segmentation using a self-supervised learning (SSL) framework based on a student-teacher architecture. Our model is pretrained on a large, unlabeled dataset of CT and MRI scans, leveraging the xLSTM backbone to capture long-range spatial dependencies and complex anatomical structures in 3D medical images. By incorporating multi-modal pretraining, our approach ensures strong generalization across both CT and MRI modalities, mitigating modality-specific variations and improving segmentation accuracy in diverse clinical settings. The use of large-scale unlabeled data significantly reduces the dependency on manual annotations, enabling robust performance even with limited labeled data. We further introduce an xLSTM-UNet-based architecture for downstream whole-heart segmentation tasks, demonstrating its effectiveness on few-label CT and MRI datasets. Our results validate the robustness and adaptability of the proposed model, highlighting its potential for advancing automated whole-heart segmentation in medical imaging.

Survival risk stratification is an important step in clinical decision making for breast cancer management. We propose a novel deep learning approach for this purpose by integrating histopathological imaging, genetic and clinical data. It employs vision transformers, specifically the MaxViT model, for image feature extraction, and self-attention to capture intricate image relationships at the patient level. A dual cross-attention mechanism fuses these features with genetic data, while clinical data is incorporated at the final layer to enhance predictive accuracy. Experiments on the public TCGA-BRCA dataset show that our model, trained using the negative log likelihood loss function, can achieve superior performance with a mean C-index of 0.64, surpassing existing methods. This advancement facilitates tailored treatment strategies, potentially leading to improved patient outcomes.

Image datasets are essential not only in validating existing methods in computer vision but also in developing new methods. Most existing image datasets focus on trichromatic intensity images to mimic human vision. However, polarization and spectrum, the wave properties of light that animals in harsh environments and with limited brain capacity often rely on, remain underrepresented in existing datasets. Although spectro-polarimetric datasets exist, these datasets have insufficient object diversity, limited illumination conditions, linear-only polarization data, and inadequate image count. Here, we introduce two spectro-polarimetric datasets: trichromatic Stokes images and hyperspectral Stokes images. These novel datasets encompass both linear and circular polarization; they introduce multiple spectral channels; and they feature a broad selection of real-world scenes. With our dataset in hand, we analyze the spectro-polarimetric image statistics, develop efficient representations of such high-dimensional data, and evaluate spectral dependency of shape-from-polarization methods. As such, the proposed dataset promises a foundation for data-driven spectro-polarimetric imaging and vision research. Dataset and code will be publicly available.

In April to May 2023, the superBIT telescope was lifted to the Earth's stratosphere by a helium-filled super-pressure balloon, to acquire astronomical imaging from above (99.5% of) the Earth's atmosphere. It was launched from New Zealand then, for 40 days, circumnavigated the globe five times at a latitude 40 to 50 degrees South. Attached to the telescope were four 'DRS' (Data Recovery System) capsules containing 5 TB solid state data storage, plus a GNSS receiver, Iridium transmitter, and parachute. Data from the telescope were copied to these, and two were dropped over Argentina. They drifted 61 km horizontally while they descended 32 km, but we predicted their descent vectors within 2.4 km: in this location, the discrepancy appears irreducible below 2 km because of high speed, gusty winds and local topography. The capsules then reported their own locations to within a few metres. We recovered the capsules and successfully retrieved all of superBIT's data - despite the telescope itself being later destroyed on landing.

We present detailed morphology measurements for 8.67 million galaxies in the DESI Legacy Imaging Surveys (DECaLS, MzLS, and BASS, plus DES). These are automated measurements made by deep learning models trained on Galaxy Zoo volunteer votes. Our models typically predict the fraction of volunteers selecting each answer to within 5-10\% for every answer to every GZ question. The models are trained on newly-collected votes for DESI-LS DR8 images as well as historical votes from GZ DECaLS. We also release the newly-collected votes. Extending our morphology measurements outside of the previously-released DECaLS/SDSS intersection increases our sky coverage by a factor of 4 (5,000 to 19,000 deg^2) and allows for full overlap with complementary surveys including ALFALFA and MaNGA.

Recent work has investigated the distributions of learned convolution filters through a large-scale study containing hundreds of heterogeneous image models. Surprisingly, on average, the distributions only show minor drifts in comparisons of various studied dimensions including the learned task, image domain, or dataset. However, among the studied image domains, medical imaging models appeared to show significant outliers through "spikey" distributions, and, therefore, learn clusters of highly specific filters different from other domains. Following this observation, we study the collected medical imaging models in more detail. We show that instead of fundamental differences, the outliers are due to specific processing in some architectures. Quite the contrary, for standardized architectures, we find that models trained on medical data do not significantly differ in their filter distributions from similar architectures trained on data from other domains. Our conclusions reinforce previous hypotheses stating that pre-training of imaging models can be done with any kind of diverse image data.

Model-based reconstruction employing the time separation technique (TST) was found to improve dynamic perfusion imaging of the liver using C-arm cone-beam computed tomography (CBCT). To apply TST using prior knowledge extracted from CT perfusion data, the liver should be accurately segmented from the CT scans. Reconstructions of primary and model-based CBCT data need to be segmented for proper visualisation and interpretation of perfusion maps. This research proposes Turbolift learning, which trains a modified version of the multi-scale Attention UNet on different liver segmentation tasks serially, following the order of the trainings CT, CBCT, CBCT TST - making the previous trainings act as pre-training stages for the subsequent ones - addressing the problem of limited number of datasets for training. For the final task of liver segmentation from CBCT TST, the proposed method achieved an overall Dice scores of 0.874pm0.031 and 0.905pm0.007 in 6-fold and 4-fold cross-validation experiments, respectively - securing statistically significant improvements over the model, which was trained only for that task. Experiments revealed that Turbolift not only improves the overall performance of the model but also makes it robust against artefacts originating from the embolisation materials and truncation artefacts. Additionally, in-depth analyses confirmed the order of the segmentation tasks. This paper shows the potential of segmenting the liver from CT, CBCT, and CBCT TST, learning from the available limited training data, which can possibly be used in the future for the visualisation and evaluation of the perfusion maps for the treatment evaluation of liver diseases.

After being collected for patient care, Observational Health Data (OHD) can further benefit patient well-being by sustaining the development of health informatics and medical research. Vast potential is unexploited because of the fiercely private nature of patient-related data and regulations to protect it. Generative Adversarial Networks (GANs) have recently emerged as a groundbreaking way to learn generative models that produce realistic synthetic data. They have revolutionized practices in multiple domains such as self-driving cars, fraud detection, digital twin simulations in industrial sectors, and medical imaging. The digital twin concept could readily apply to modelling and quantifying disease progression. In addition, GANs posses many capabilities relevant to common problems in healthcare: lack of data, class imbalance, rare diseases, and preserving privacy. Unlocking open access to privacy-preserving OHD could be transformative for scientific research. In the midst of COVID-19, the healthcare system is facing unprecedented challenges, many of which of are data related for the reasons stated above. Considering these facts, publications concerning GAN applied to OHD seemed to be severely lacking. To uncover the reasons for this slow adoption, we broadly reviewed the published literature on the subject. Our findings show that the properties of OHD were initially challenging for the existing GAN algorithms (unlike medical imaging, for which state-of-the-art model were directly transferable) and the evaluation synthetic data lacked clear metrics. We find more publications on the subject than expected, starting slowly in 2017, and since then at an increasing rate. The difficulties of OHD remain, and we discuss issues relating to evaluation, consistency, benchmarking, data modelling, and reproducibility.

Multimodal large language models (MLLMs) hold significant potential in the medical field, but their capabilities are often limited by insufficient data in certain medical domains, highlighting the need for understanding what kinds of images can be used by MLLMs for generalization. Current research suggests that multi-task training outperforms single-task as different tasks can benefit each other, but they often overlook the internal relationships within these tasks, providing limited guidance on selecting datasets to enhance specific tasks. To analyze this phenomenon, we attempted to employ compositional generalization (CG)-the ability of models to understand novel combinations by recombining learned elements-as a guiding framework. Since medical images can be precisely defined by Modality, Anatomical area, and Task, naturally providing an environment for exploring CG. Therefore, we assembled 106 medical datasets to create Med-MAT for comprehensive experiments. The experiments confirmed that MLLMs can use CG to understand unseen medical images and identified CG as one of the main drivers of the generalization observed in multi-task training. Additionally, further studies demonstrated that CG effectively supports datasets with limited data and delivers consistent performance across different backbones, highlighting its versatility and broad applicability. Med-MAT is publicly available at https://github.com/FreedomIntelligence/Med-MAT.

Existing vision-text contrastive learning models enhance representation transferability and support zero-shot prediction by matching paired image and caption embeddings while pushing unrelated pairs apart. However, astronomical image-label datasets are significantly smaller compared to general image and label datasets available from the internet. We introduce CosmoCLIP, an astronomical image-text contrastive learning framework precisely fine-tuned on the pre-trained CLIP model using SpaceNet and BLIP-based captions. SpaceNet, attained via FLARE, constitutes ~13k optimally distributed images, while BLIP acts as a rich knowledge extractor. The rich semantics derived from this SpaceNet and BLIP descriptions, when learned contrastively, enable CosmoCLIP to achieve superior generalization across various in-domain and out-of-domain tasks. Our results demonstrate that CosmoCLIP is a straightforward yet powerful framework, significantly outperforming CLIP in zero-shot classification and image-text retrieval tasks.

We present ReXGradient-160K, representing the largest publicly available chest X-ray dataset to date in terms of the number of patients. This dataset contains 160,000 chest X-ray studies with paired radiological reports from 109,487 unique patients across 3 U.S. health systems (79 medical sites). This comprehensive dataset includes multiple images per study and detailed radiology reports, making it particularly valuable for the development and evaluation of AI systems for medical imaging and automated report generation models. The dataset is divided into training (140,000 studies), validation (10,000 studies), and public test (10,000 studies) sets, with an additional private test set (10,000 studies) reserved for model evaluation on the ReXrank benchmark. By providing this extensive dataset, we aim to accelerate research in medical imaging AI and advance the state-of-the-art in automated radiological analysis. Our dataset will be open-sourced at https://huggingface.co/datasets/rajpurkarlab/ReXGradient-160K.

Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the performance of computational imaging systems, especially those that incorporate machine learning, is sample-dependent. Thus, standardized datasets are an essential tool for comparing the performance of different approaches. Here, we introduce the Berkeley Single Cell Computational Microscopy (BSCCM) dataset, which contains over ~12,000,000 images of 400,000 of individual white blood cells. The dataset contains images captured with multiple illumination patterns on an LED array microscope and fluorescent measurements of the abundance of surface proteins that mark different cell types. We hope this dataset will provide a valuable resource for the development and testing of new algorithms in computational microscopy and computer vision with practical biomedical applications.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. Here we introduce BrainFM, a modality-agnostic, multi-task vision foundation model for human brain imaging. With the proposed "mild-to-severe" intra-subject generation and "real-synth" mix-up training strategy, BrainFM is resilient to the appearance of acquired images (e.g., modality, contrast, deformation, resolution, artifacts), and can be directly applied to five fundamental brain imaging tasks, including image synthesis for CT and T1w/T2w/FLAIR MRI, anatomy segmentation, scalp-to-cortical distance, bias field estimation, and registration. We evaluate the efficacy of BrainFM on eleven public datasets, and demonstrate its robustness and effectiveness across all tasks and input modalities. Code is available at https://github.com/jhuldr/BrainFM.

Most papers caution against using predictive models for disease stratification based on unselected radiomic features, as these features are affected by contouring variability. Instead, they advocate for the use of the Intraclass Correlation Coefficient (ICC) as a measure of stability for feature selection. However, the direct effect of segmentation variability on the predictive models is rarely studied. This study investigates the impact of segmentation variability on feature stability and predictive performance in radiomics-based prediction of Triple-Negative Breast Cancer (TNBC) subtype using Magnetic Resonance Imaging. A total of 244 images from the Duke dataset were used, with segmentation variability introduced through modifications of manual segmentations. For each mask, explainable radiomic features were selected using the Shapley Additive exPlanations method and used to train logistic regression models. Feature stability across segmentations was assessed via ICC, Pearson's correlation, and reliability scores quantifying the relationship between feature stability and segmentation variability. Results indicate that segmentation accuracy does not significantly impact predictive performance. While incorporating peritumoral information may reduce feature reproducibility, it does not diminish feature predictive capability. Moreover, feature selection in predictive models is not inherently tied to feature stability with respect to segmentation, suggesting that an overreliance on ICC or reliability scores for feature selection might exclude valuable predictive features.

With the rapid advancement of deep learning, particularly in the field of medical image analysis, an increasing number of Vision-Language Models (VLMs) are being widely applied to solve complex health and biomedical challenges. However, existing research has primarily focused on specific tasks or single modalities, which limits their applicability and generalization across diverse medical scenarios. To address this challenge, we propose UMIT, a unified multi-modal, multi-task VLM designed specifically for medical imaging tasks. UMIT is able to solve various tasks, including visual question answering, disease detection, and medical report generation. In addition, it is applicable to multiple imaging modalities (e.g., X-ray, CT and PET), covering a wide range of applications from basic diagnostics to complex lesion analysis. Moreover, UMIT supports both English and Chinese, expanding its applicability globally and ensuring accessibility to healthcare services in different linguistic contexts. To enhance the model's adaptability and task-handling capability, we design a unique two-stage training strategy and fine-tune UMIT with designed instruction templates. Through extensive empirical evaluation, UMIT outperforms previous methods in five tasks across multiple datasets. The performance of UMIT indicates that it can significantly enhance diagnostic accuracy and workflow efficiency, thus providing effective solutions for medical imaging applications.

Most existing learning-based methods for solving imaging inverse problems can be roughly divided into two classes: iterative algorithms, such as plug-and-play and diffusion methods, that leverage pretrained denoisers, and unrolled architectures that are trained end-to-end for specific imaging problems. Iterative methods in the first class are computationally costly and often provide suboptimal reconstruction performance, whereas unrolled architectures are generally specific to a single inverse problem and require expensive training. In this work, we propose a novel non-iterative, lightweight architecture that incorporates knowledge about the forward operator (acquisition physics and noise parameters) without relying on unrolling. Our model is trained to solve a wide range of inverse problems beyond denoising, including deblurring, magnetic resonance imaging, computed tomography, inpainting, and super-resolution. The proposed model can be easily adapted to unseen inverse problems or datasets with a few fine-tuning steps (up to a few images) in a self-supervised way, without ground-truth references. Throughout a series of experiments, we demonstrate state-of-the-art performance from medical imaging to low-photon imaging and microscopy.

Learning based single image super resolution (SISR) task is well investigated in 2D images. However, SISR for 3D Magnetics Resonance Images (MRI) is more challenging compared to 2D, mainly due to the increased number of neural network parameters, the larger memory requirement and the limited amount of available training data. Current SISR methods for 3D volumetric images are based on Generative Adversarial Networks (GANs), especially Wasserstein GANs due to their training stability. Other common architectures in the 2D domain, e.g. transformer models, require large amounts of training data and are therefore not suitable for the limited 3D data. However, Wasserstein GANs can be problematic because they may not converge to a global optimum and thus produce blurry results. Here, we propose a new method for 3D SR based on the GAN framework. Specifically, we use instance noise to balance the GAN training. Furthermore, we use a relativistic GAN loss function and an updating feature extractor during the training process. We show that our method produces highly accurate results. We also show that we need very few training samples. In particular, we need less than 30 samples instead of thousands of training samples that are typically required in previous studies. Finally, we show improved out-of-sample results produced by our model.

The success of automated medical image analysis depends on large-scale and expert-annotated training sets. Unsupervised domain adaptation (UDA) has been raised as a promising approach to alleviate the burden of labeled data collection. However, they generally operate under the closed-set adaptation setting assuming an identical label set between the source and target domains, which is over-restrictive in clinical practice where new classes commonly exist across datasets due to taxonomic inconsistency. While several methods have been presented to tackle both domain shifts and incoherent label sets, none of them take into account the common characteristics of the two issues and consider the learning dynamics along network training. In this work, we propose optimization trajectory distillation, a unified approach to address the two technical challenges from a new perspective. It exploits the low-rank nature of gradient space and devises a dual-stream distillation algorithm to regularize the learning dynamics of insufficiently annotated domain and classes with the external guidance obtained from reliable sources. Our approach resolves the issue of inadequate navigation along network optimization, which is the major obstacle in the taxonomy adaptive cross-domain adaptation scenario. We evaluate the proposed method extensively on several tasks towards various endpoints with clinical and open-world significance. The results demonstrate its effectiveness and improvements over previous methods.

Purpose: This study aims to explore training strategies to improve convolutional neural network-based image-to-image deformable registration for abdominal imaging. Methods: Different training strategies, loss functions, and transfer learning schemes were considered. Furthermore, an augmentation layer which generates artificial training image pairs on-the-fly was proposed, in addition to a loss layer that enables dynamic loss weighting. Results: Guiding registration using segmentations in the training step proved beneficial for deep-learning-based image registration. Finetuning the pretrained model from the brain MRI dataset to the abdominal CT dataset further improved performance on the latter application, removing the need for a large dataset to yield satisfactory performance. Dynamic loss weighting also marginally improved performance, all without impacting inference runtime. Conclusion: Using simple concepts, we improved the performance of a commonly used deep image registration architecture, VoxelMorph. In future work, our framework, DDMR, should be validated on different datasets to further assess its value.

Federated learning (FL) is a distributed learning method that offers medical institutes the prospect of collaboration in a global model while preserving the privacy of their patients. Although most medical centers conduct similar medical imaging tasks, their differences, such as specializations, number of patients, and devices, lead to distinctive data distributions. Data heterogeneity poses a challenge for FL and the personalization of the local models. In this work, we investigate an adaptive hierarchical clustering method for FL to produce intermediate semi-global models, so clients with similar data distribution have the chance of forming a more specialized model. Our method forms several clusters consisting of clients with the most similar data distributions; then, each cluster continues to train separately. Inside the cluster, we use meta-learning to improve the personalization of the participants' models. We compare the clustering approach with classical FedAvg and centralized training by evaluating our proposed methods on the HAM10k dataset for skin lesion classification with extreme heterogeneous data distribution. Our experiments demonstrate significant performance gain in heterogeneous distribution compared to standard FL methods in classification accuracy. Moreover, we show that the models converge faster if applied in clusters and outperform centralized training while using only a small subset of data.

Deep neural networks have enabled improved image quality and fast inference times for various inverse problems, including accelerated magnetic resonance imaging (MRI) reconstruction. However, such models require a large number of fully-sampled ground truth datasets, which are difficult to curate, and are sensitive to distribution drifts. In this work, we propose applying physics-driven data augmentations for consistency training that leverage our domain knowledge of the forward MRI data acquisition process and MRI physics to achieve improved label efficiency and robustness to clinically-relevant distribution drifts. Our approach, termed VORTEX, (1) demonstrates strong improvements over supervised baselines with and without data augmentation in robustness to signal-to-noise ratio change and motion corruption in data-limited regimes; (2) considerably outperforms state-of-the-art purely image-based data augmentation techniques and self-supervised reconstruction methods on both in-distribution and out-of-distribution data; and (3) enables composing heterogeneous image-based and physics-driven data augmentations. Our code is available at https://github.com/ad12/meddlr.

Federated learning (FL) has been a promising approach in the field of medical imaging in recent years. A critical problem in FL, specifically in medical scenarios is to have a more accurate shared model which is robust to noisy and out-of distribution clients. In this work, we tackle the problem of statistical heterogeneity in data for FL which is highly plausible in medical data where for example the data comes from different sites with different scanner settings. We propose IDA (Inverse Distance Aggregation), a novel adaptive weighting approach for clients based on meta-information which handles unbalanced and non-iid data. We extensively analyze and evaluate our method against the well-known FL approach, Federated Averaging as a baseline.