Daily Papers

This paper introduces a network for volumetric segmentation that learns from sparsely annotated volumetric images. We outline two attractive use cases of this method: (1) In a semi-automated setup, the user annotates some slices in the volume to be segmented. The network learns from these sparse annotations and provides a dense 3D segmentation. (2) In a fully-automated setup, we assume that a representative, sparsely annotated training set exists. Trained on this data set, the network densely segments new volumetric images. The proposed network extends the previous u-net architecture from Ronneberger et al. by replacing all 2D operations with their 3D counterparts. The implementation performs on-the-fly elastic deformations for efficient data augmentation during training. It is trained end-to-end from scratch, i.e., no pre-trained network is required. We test the performance of the proposed method on a complex, highly variable 3D structure, the Xenopus kidney, and achieve good results for both use cases.

We propose combining memory saving techniques with traditional U-Net architectures to increase the complexity of the models on the Brain Tumor Segmentation (BraTS) challenge. The BraTS challenge consists of a 3D segmentation of a 240x240x155x4 input image into a set of tumor classes. Because of the large volume and need for 3D convolutional layers, this task is very memory intensive. To address this, prior approaches use smaller cropped images while constraining the model's depth and width. Our 3D U-Net uses a reversible version of the mobile inverted bottleneck block defined in MobileNetV2, MnasNet and the more recent EfficientNet architectures to save activation memory during training. Using reversible layers enables the model to recompute input activations given the outputs of that layer, saving memory by eliminating the need to store activations during the forward pass. The inverted residual bottleneck block uses lightweight depthwise separable convolutions to reduce computation by decomposing convolutions into a pointwise convolution and a depthwise convolution. Further, this block inverts traditional bottleneck blocks by placing an intermediate expansion layer between the input and output linear 1x1 convolution, reducing the total number of channels. Given a fixed memory budget, with these memory saving techniques, we are able to train image volumes up to 3x larger, models with 25% more depth, or models with up to 2x the number of channels than a corresponding non-reversible network.

Accurate segmentation of brain tumors plays a key role in the diagnosis and treatment of brain tumor diseases. It serves as a critical technology for quantifying tumors and extracting their features. With the increasing application of deep learning methods, the computational burden has become progressively heavier. To achieve a lightweight model with good segmentation performance, this study proposes the MBDRes-U-Net model using the three-dimensional (3D) U-Net codec framework, which integrates multibranch residual blocks and fused attention into the model. The computational burden of the model is reduced by the branch strategy, which effectively uses the rich local features in multimodal images and enhances the segmentation performance of subtumor regions. Additionally, during encoding, an adaptive weighted expansion convolution layer is introduced into the multi-branch residual block, which enriches the feature expression and improves the segmentation accuracy of the model. Experiments on the Brain Tumor Segmentation (BraTS) Challenge 2018 and 2019 datasets show that the architecture could maintain a high precision of brain tumor segmentation while considerably reducing the calculation overhead.Our code is released at https://github.com/Huaibei-normal-university-cv-laboratory/mbdresunet

Automatic and consistent meningioma segmentation in T1-weighted MRI volumes and corresponding volumetric assessment is of use for diagnosis, treatment planning, and tumor growth evaluation. In this paper, we optimized the segmentation and processing speed performances using a large number of both surgically treated meningiomas and untreated meningiomas followed at the outpatient clinic. We studied two different 3D neural network architectures: (i) a simple encoder-decoder similar to a 3D U-Net, and (ii) a lightweight multi-scale architecture (PLS-Net). In addition, we studied the impact of different training schemes. For the validation studies, we used 698 T1-weighted MR volumes from St. Olav University Hospital, Trondheim, Norway. The models were evaluated in terms of detection accuracy, segmentation accuracy and training/inference speed. While both architectures reached a similar Dice score of 70% on average, the PLS-Net was more accurate with an F1-score of up to 88%. The highest accuracy was achieved for the largest meningiomas. Speed-wise, the PLS-Net architecture tended to converge in about 50 hours while 130 hours were necessary for U-Net. Inference with PLS-Net takes less than a second on GPU and about 15 seconds on CPU. Overall, with the use of mixed precision training, it was possible to train competitive segmentation models in a relatively short amount of time using the lightweight PLS-Net architecture. In the future, the focus should be brought toward the segmentation of small meningiomas (less than 2ml) to improve clinical relevance for automatic and early diagnosis as well as speed of growth estimates.

3D Gaussian Splatting (GS) have achieved considerable improvement over Neural Radiance Fields in terms of 3D fitting fidelity and rendering speed. However, this unstructured representation with scattered Gaussians poses a significant challenge for generative modeling. To address the problem, we introduce GaussianCube, a structured GS representation that is both powerful and efficient for generative modeling. We achieve this by first proposing a modified densification-constrained GS fitting algorithm which can yield high-quality fitting results using a fixed number of free Gaussians, and then re-arranging the Gaussians into a predefined voxel grid via Optimal Transport. The structured grid representation allows us to use standard 3D U-Net as our backbone in diffusion generative modeling without elaborate designs. Extensive experiments conducted on ShapeNet and OmniObject3D show that our model achieves state-of-the-art generation results both qualitatively and quantitatively, underscoring the potential of GaussianCube as a powerful and versatile 3D representation.

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.

This paper introduces a pioneering 3D volumetric encoder designed for text-to-3D generation. To scale up the training data for the diffusion model, a lightweight network is developed to efficiently acquire feature volumes from multi-view images. The 3D volumes are then trained on a diffusion model for text-to-3D generation using a 3D U-Net. This research further addresses the challenges of inaccurate object captions and high-dimensional feature volumes. The proposed model, trained on the public Objaverse dataset, demonstrates promising outcomes in producing diverse and recognizable samples from text prompts. Notably, it empowers finer control over object part characteristics through textual cues, fostering model creativity by seamlessly combining multiple concepts within a single object. This research significantly contributes to the progress of 3D generation by introducing an efficient, flexible, and scalable representation methodology. Code is available at https://github.com/tzco/VolumeDiffusion.

We present an efficient text-to-video generation framework based on latent diffusion models, termed MagicVideo. Given a text description, MagicVideo can generate photo-realistic video clips with high relevance to the text content. With the proposed efficient latent 3D U-Net design, MagicVideo can generate video clips with 256x256 spatial resolution on a single GPU card, which is 64x faster than the recent video diffusion model (VDM). Unlike previous works that train video generation from scratch in the RGB space, we propose to generate video clips in a low-dimensional latent space. We further utilize all the convolution operator weights of pre-trained text-to-image generative U-Net models for faster training. To achieve this, we introduce two new designs to adapt the U-Net decoder to video data: a framewise lightweight adaptor for the image-to-video distribution adjustment and a directed temporal attention module to capture frame temporal dependencies. The whole generation process is within the low-dimension latent space of a pre-trained variation auto-encoder. We demonstrate that MagicVideo can generate both realistic video content and imaginary content in a photo-realistic style with a trade-off in terms of quality and computational cost. Refer to https://magicvideo.github.io/# for more examples.

Recent advances in the diffusion models have significantly improved text-to-image generation. However, generating videos from text is a more challenging task than generating images from text, due to the much larger dataset and higher computational cost required. Most existing video generation methods use either a 3D U-Net architecture that considers the temporal dimension or autoregressive generation. These methods require large datasets and are limited in terms of computational costs compared to text-to-image generation. To tackle these challenges, we propose a simple but effective novel grid diffusion for text-to-video generation without temporal dimension in architecture and a large text-video paired dataset. We can generate a high-quality video using a fixed amount of GPU memory regardless of the number of frames by representing the video as a grid image. Additionally, since our method reduces the dimensions of the video to the dimensions of the image, various image-based methods can be applied to videos, such as text-guided video manipulation from image manipulation. Our proposed method outperforms the existing methods in both quantitative and qualitative evaluations, demonstrating the suitability of our model for real-world video generation.

The motion transfer task involves transferring motion from a source video to newly generated videos, requiring the model to decouple motion from appearance. Previous diffusion-based methods primarily rely on separate spatial and temporal attention mechanisms within 3D U-Net. In contrast, state-of-the-art video Diffusion Transformers (DiT) models use 3D full attention, which does not explicitly separate temporal and spatial information. Thus, the interaction between spatial and temporal dimensions makes decoupling motion and appearance more challenging for DiT models. In this paper, we propose DeT, a method that adapts DiT models to improve motion transfer ability. Our approach introduces a simple yet effective temporal kernel to smooth DiT features along the temporal dimension, facilitating the decoupling of foreground motion from background appearance. Meanwhile, the temporal kernel effectively captures temporal variations in DiT features, which are closely related to motion. Moreover, we introduce explicit supervision along dense trajectories in the latent feature space to further enhance motion consistency. Additionally, we present MTBench, a general and challenging benchmark for motion transfer. We also introduce a hybrid motion fidelity metric that considers both the global and local motion similarity. Therefore, our work provides a more comprehensive evaluation than previous works. Extensive experiments on MTBench demonstrate that DeT achieves the best trade-off between motion fidelity and edit fidelity.

Natural data is redundant yet predominant architectures tile computation uniformly across their input and output space. We propose the Recurrent Interface Networks (RINs), an attention-based architecture that decouples its core computation from the dimensionality of the data, enabling adaptive computation for more scalable generation of high-dimensional data. RINs focus the bulk of computation (i.e. global self-attention) on a set of latent tokens, using cross-attention to read and write (i.e. route) information between latent and data tokens. Stacking RIN blocks allows bottom-up (data to latent) and top-down (latent to data) feedback, leading to deeper and more expressive routing. While this routing introduces challenges, this is less problematic in recurrent computation settings where the task (and routing problem) changes gradually, such as iterative generation with diffusion models. We show how to leverage recurrence by conditioning the latent tokens at each forward pass of the reverse diffusion process with those from prior computation, i.e. latent self-conditioning. RINs yield state-of-the-art pixel diffusion models for image and video generation, scaling to 1024X1024 images without cascades or guidance, while being domain-agnostic and up to 10X more efficient than 2D and 3D U-Nets.

Convolutional neural networks (CNNs) are the current state-of-the-art meta-algorithm for volumetric segmentation of medical data, for example, to localize COVID-19 infected tissue on computer tomography scans or the detection of tumour volumes in magnetic resonance imaging. A key limitation of 3D CNNs on voxelised data is that the memory consumption grows cubically with the training data resolution. Occupancy networks (O-Nets) are an alternative for which the data is represented continuously in a function space and 3D shapes are learned as a continuous decision boundary. While O-Nets are significantly more memory efficient than 3D CNNs, they are limited to simple shapes, are relatively slow at inference, and have not yet been adapted for 3D semantic segmentation of medical data. Here, we propose Occupancy Networks for Semantic Segmentation (OSS-Nets) to accurately and memory-efficiently segment 3D medical data. We build upon the original O-Net with modifications for increased expressiveness leading to improved segmentation performance comparable to 3D CNNs, as well as modifications for faster inference. We leverage local observations to represent complex shapes and prior encoder predictions to expedite inference. We showcase OSS-Net's performance on 3D brain tumour and liver segmentation against a function space baseline (O-Net), a performance baseline (3D residual U-Net), and an efficiency baseline (2D residual U-Net). OSS-Net yields segmentation results similar to the performance baseline and superior to the function space and efficiency baselines. In terms of memory efficiency, OSS-Net consumes comparable amounts of memory as the function space baseline, somewhat more memory than the efficiency baseline and significantly less than the performance baseline. As such, OSS-Net enables memory-efficient and accurate 3D semantic segmentation that can scale to high resolutions.

The high cure rate of cancer is inextricably linked to physicians' accuracy in diagnosis and treatment, therefore a model that can accomplish high-precision tumor segmentation has become a necessity in many applications of the medical industry. It can effectively lower the rate of misdiagnosis while considerably lessening the burden on clinicians. However, fully automated target organ segmentation is problematic due to the irregular stereo structure of 3D volume organs. As a basic model for this class of real applications, U-Net excels. It can learn certain global and local features, but still lacks the capacity to grasp spatial long-range relationships and contextual information at multiple scales. This paper proposes a tumor segmentation model MPU-Net for patient volume CT images, which is inspired by Transformer with a global attention mechanism. By combining image serialization with the Position Attention Module, the model attempts to comprehend deeper contextual dependencies and accomplish precise positioning. Each layer of the decoder is also equipped with a multi-scale module and a cross-attention mechanism. The capability of feature extraction and integration at different levels has been enhanced, and the hybrid loss function developed in this study can better exploit high-resolution characteristic information. Moreover, the suggested architecture is tested and evaluated on the Liver Tumor Segmentation Challenge 2017 (LiTS 2017) dataset. Compared with the benchmark model U-Net, MPU-Net shows excellent segmentation results. The dice, accuracy, precision, specificity, IOU, and MCC metrics for the best model segmentation results are 92.17%, 99.08%, 91.91%, 99.52%, 85.91%, and 91.74%, respectively. Outstanding indicators in various aspects illustrate the exceptional performance of this framework in automatic medical image segmentation.

The release of nnU-Net marked a paradigm shift in 3D medical image segmentation, demonstrating that a properly configured U-Net architecture could still achieve state-of-the-art results. Despite this, the pursuit of novel architectures, and the respective claims of superior performance over the U-Net baseline, continued. In this study, we demonstrate that many of these recent claims fail to hold up when scrutinized for common validation shortcomings, such as the use of inadequate baselines, insufficient datasets, and neglected computational resources. By meticulously avoiding these pitfalls, we conduct a thorough and comprehensive benchmarking of current segmentation methods including CNN-based, Transformer-based, and Mamba-based approaches. In contrast to current beliefs, we find that the recipe for state-of-the-art performance is 1) employing CNN-based U-Net models, including ResNet and ConvNeXt variants, 2) using the nnU-Net framework, and 3) scaling models to modern hardware resources. These results indicate an ongoing innovation bias towards novel architectures in the field and underscore the need for more stringent validation standards in the quest for scientific progress.

Computer-aided medical image segmentation has been applied widely in diagnosis and treatment to obtain clinically useful information of shapes and volumes of target organs and tissues. In the past several years, convolutional neural network (CNN) based methods (e.g., U-Net) have dominated this area, but still suffered from inadequate long-range information capturing. Hence, recent work presented computer vision Transformer variants for medical image segmentation tasks and obtained promising performances. Such Transformers model long-range dependency by computing pair-wise patch relations. However, they incur prohibitive computational costs, especially on 3D medical images (e.g., CT and MRI). In this paper, we propose a new method called Dilated Transformer, which conducts self-attention for pair-wise patch relations captured alternately in local and global scopes. Inspired by dilated convolution kernels, we conduct the global self-attention in a dilated manner, enlarging receptive fields without increasing the patches involved and thus reducing computational costs. Based on this design of Dilated Transformer, we construct a U-shaped encoder-decoder hierarchical architecture called D-Former for 3D medical image segmentation. Experiments on the Synapse and ACDC datasets show that our D-Former model, trained from scratch, outperforms various competitive CNN-based or Transformer-based segmentation models at a low computational cost without time-consuming per-training process.

Recent Diffusion Transformers (e.g., DiT) have demonstrated their powerful effectiveness in generating high-quality 2D images. However, it is still being determined whether the Transformer architecture performs equally well in 3D shape generation, as previous 3D diffusion methods mostly adopted the U-Net architecture. To bridge this gap, we propose a novel Diffusion Transformer for 3D shape generation, namely DiT-3D, which can directly operate the denoising process on voxelized point clouds using plain Transformers. Compared to existing U-Net approaches, our DiT-3D is more scalable in model size and produces much higher quality generations. Specifically, the DiT-3D adopts the design philosophy of DiT but modifies it by incorporating 3D positional and patch embeddings to adaptively aggregate input from voxelized point clouds. To reduce the computational cost of self-attention in 3D shape generation, we incorporate 3D window attention into Transformer blocks, as the increased 3D token length resulting from the additional dimension of voxels can lead to high computation. Finally, linear and devoxelization layers are used to predict the denoised point clouds. In addition, our transformer architecture supports efficient fine-tuning from 2D to 3D, where the pre-trained DiT-2D checkpoint on ImageNet can significantly improve DiT-3D on ShapeNet. Experimental results on the ShapeNet dataset demonstrate that the proposed DiT-3D achieves state-of-the-art performance in high-fidelity and diverse 3D point cloud generation. In particular, our DiT-3D decreases the 1-Nearest Neighbor Accuracy of the state-of-the-art method by 4.59 and increases the Coverage metric by 3.51 when evaluated on Chamfer Distance.

3D content creation has achieved significant progress in terms of both quality and speed. Although current feed-forward models can produce 3D objects in seconds, their resolution is constrained by the intensive computation required during training. In this paper, we introduce Large Multi-View Gaussian Model (LGM), a novel framework designed to generate high-resolution 3D models from text prompts or single-view images. Our key insights are two-fold: 1) 3D Representation: We propose multi-view Gaussian features as an efficient yet powerful representation, which can then be fused together for differentiable rendering. 2) 3D Backbone: We present an asymmetric U-Net as a high-throughput backbone operating on multi-view images, which can be produced from text or single-view image input by leveraging multi-view diffusion models. Extensive experiments demonstrate the high fidelity and efficiency of our approach. Notably, we maintain the fast speed to generate 3D objects within 5 seconds while boosting the training resolution to 512, thereby achieving high-resolution 3D content generation.

Transcranial focused ultrasound (tFUS) is an emerging modality for non-invasive brain stimulation and therapeutic intervention, offering millimeter-scale spatial precision and the ability to target deep brain structures. However, the heterogeneous and anisotropic nature of the human skull introduces significant distortions to the propagating ultrasound wavefront, which require time-consuming patient-specific planning and corrections using numerical solvers for accurate targeting. To enable data-driven approaches in this domain, we introduce TFUScapes, the first large-scale, high-resolution dataset of tFUS simulations through anatomically realistic human skulls derived from T1-weighted MRI images. We have developed a scalable simulation engine pipeline using the k-Wave pseudo-spectral solver, where each simulation returns a steady-state pressure field generated by a focused ultrasound transducer placed at realistic scalp locations. In addition to the dataset, we present DeepTFUS, a deep learning model that estimates normalized pressure fields directly from input 3D CT volumes and transducer position. The model extends a U-Net backbone with transducer-aware conditioning, incorporating Fourier-encoded position embeddings and MLP layers to create global transducer embeddings. These embeddings are fused with U-Net encoder features via feature-wise modulation, dynamic convolutions, and cross-attention mechanisms. The model is trained using a combination of spatially weighted and gradient-sensitive loss functions, enabling it to approximate high-fidelity wavefields. The TFUScapes dataset is publicly released to accelerate research at the intersection of computational acoustics, neurotechnology, and deep learning. The project page is available at https://github.com/CAMMA-public/TFUScapes.

IceCloudNet is a novel method based on machine learning able to predict high-quality vertically resolved cloud ice water contents (IWC) and ice crystal number concentrations (N_ice). The predictions come at the spatio-temporal coverage and resolution of geostationary satellite observations (SEVIRI) and the vertical resolution of active satellite retrievals (DARDAR). IceCloudNet consists of a ConvNeXt-based U-Net and a 3D PatchGAN discriminator model and is trained by predicting DARDAR profiles from co-located SEVIRI images. Despite the sparse availability of DARDAR data due to its narrow overpass, IceCloudNet is able to predict cloud occurrence, spatial structure, and microphysical properties with high precision. The model has been applied to ten years of SEVIRI data, producing a dataset of vertically resolved IWC and N_ice of clouds containing ice with a 3 kmx3 kmx240 mx15 minute resolution in a spatial domain of 30{\deg}W to 30{\deg}E and 30{\deg}S to 30{\deg}N. The produced dataset increases the availability of vertical cloud profiles, for the period when DARDAR is available, by more than six orders of magnitude and moreover, IceCloudNet is able to produce vertical cloud profiles beyond the lifetime of the recently ended satellite missions underlying DARDAR.

Current image-to-3D approaches suffer from high computational costs and lack scalability for high-resolution outputs. In contrast, we introduce a novel framework to directly generate explicit surface geometry and texture using multi-view 2D depth and RGB images along with 3D Gaussian features using a repurposed Stable Diffusion model. We introduce a depth branch into U-Net for efficient and high quality multi-view, cross-domain generation and incorporate epipolar attention into the latent-to-pixel decoder for pixel-level multi-view consistency. By back-projecting the generated depth pixels into 3D space, we create a structured 3D representation that can be either rendered via Gaussian splatting or extracted to high-quality meshes, thereby leveraging additional novel view synthesis loss to further improve our performance. Extensive experiments demonstrate that our method surpasses existing baselines in geometry and texture quality while achieving significantly faster generation time.

Self-Supervised Learning (SSL) presents an exciting opportunity to unlock the potential of vast, untapped clinical datasets, for various downstream applications that suffer from the scarcity of labeled data. While SSL has revolutionized fields like natural language processing and computer vision, its adoption in 3D medical image computing has been limited by three key pitfalls: Small pre-training dataset sizes, architectures inadequate for 3D medical image analysis, and insufficient evaluation practices. In this paper, we address these issues by i) leveraging a large-scale dataset of 39k 3D brain MRI volumes and ii) using a Residual Encoder U-Net architecture within the state-of-the-art nnU-Net framework. iii) A robust development framework, incorporating 5 development and 8 testing brain MRI segmentation datasets, allowed performance-driven design decisions to optimize the simple concept of Masked Auto Encoders (MAEs) for 3D CNNs. The resulting model not only surpasses previous SSL methods but also outperforms the strong nnU-Net baseline by an average of approximately 3 Dice points setting a new state-of-the-art. Our code and models are made available here.

Head and neck (H&N) cancers are among the most prevalent types of cancer worldwide, and [18F]F-FDG PET/CT is widely used for H&N cancer management. Recently, the diffusion model has demonstrated remarkable performance in various image-generation tasks. In this work, we proposed a 3D diffusion model to accurately perform H&N tumor segmentation from 3D PET and CT volumes. The 3D diffusion model was developed considering the 3D nature of PET and CT images acquired. During the reverse process, the model utilized a 3D UNet structure and took the concatenation of PET, CT, and Gaussian noise volumes as the network input to generate the tumor mask. Experiments based on the HECKTOR challenge dataset were conducted to evaluate the effectiveness of the proposed diffusion model. Several state-of-the-art techniques based on U-Net and Transformer structures were adopted as the reference methods. Benefits of employing both PET and CT as the network input as well as further extending the diffusion model from 2D to 3D were investigated based on various quantitative metrics and the uncertainty maps generated. Results showed that the proposed 3D diffusion model could generate more accurate segmentation results compared with other methods. Compared to the diffusion model in 2D format, the proposed 3D model yielded superior results. Our experiments also highlighted the advantage of utilizing dual-modality PET and CT data over only single-modality data for H&N tumor segmentation.

Diffusion models have emerged as a popular method for 3D generation. However, it is still challenging for diffusion models to efficiently generate diverse and high-quality 3D shapes. In this paper, we introduce OctFusion, which can generate 3D shapes with arbitrary resolutions in 2.5 seconds on a single Nvidia 4090 GPU, and the extracted meshes are guaranteed to be continuous and manifold. The key components of OctFusion are the octree-based latent representation and the accompanying diffusion models. The representation combines the benefits of both implicit neural representations and explicit spatial octrees and is learned with an octree-based variational autoencoder. The proposed diffusion model is a unified multi-scale U-Net that enables weights and computation sharing across different octree levels and avoids the complexity of widely used cascaded diffusion schemes. We verify the effectiveness of OctFusion on the ShapeNet and Objaverse datasets and achieve state-of-the-art performances on shape generation tasks. We demonstrate that OctFusion is extendable and flexible by generating high-quality color fields for textured mesh generation and high-quality 3D shapes conditioned on text prompts, sketches, or category labels. Our code and pre-trained models are available at https://github.com/octree-nn/octfusion.

Coronary microvascular disease constitutes a substantial risk to human health. Employing computer-aided analysis and diagnostic systems, medical professionals can intervene early in disease progression, with 3D vessel segmentation serving as a crucial component. Nevertheless, conventional U-Net architectures tend to yield incoherent and imprecise segmentation outcomes, particularly for small vessel structures. While models with attention mechanisms, such as Transformers and large convolutional kernels, demonstrate superior performance, their extensive computational demands during training and inference lead to increased time complexity. In this study, we leverage Fourier domain learning as a substitute for multi-scale convolutional kernels in 3D hierarchical segmentation models, which can reduce computational expenses while preserving global receptive fields within the network. Furthermore, a zero-parameter frequency domain fusion method is designed to improve the skip connections in U-Net architecture. Experimental results on a public dataset and an in-house dataset indicate that our novel Fourier transformation-based network achieves remarkable dice performance (84.37\% on ASACA500 and 80.32\% on ImageCAS) in tubular vessel segmentation tasks and substantially reduces computational requirements without compromising global receptive fields.

3D asset generation is getting massive amounts of attention, inspired by the recent success of text-guided 2D content creation. Existing text-to-3D methods use pretrained text-to-image diffusion models in an optimization problem or fine-tune them on synthetic data, which often results in non-photorealistic 3D objects without backgrounds. In this paper, we present a method that leverages pretrained text-to-image models as a prior, and learn to generate multi-view images in a single denoising process from real-world data. Concretely, we propose to integrate 3D volume-rendering and cross-frame-attention layers into each block of the existing U-Net network of the text-to-image model. Moreover, we design an autoregressive generation that renders more 3D-consistent images at any viewpoint. We train our model on real-world datasets of objects and showcase its capabilities to generate instances with a variety of high-quality shapes and textures in authentic surroundings. Compared to the existing methods, the results generated by our method are consistent, and have favorable visual quality (-30% FID, -37% KID).

Text-guided human motion generation has drawn significant interest because of its impactful applications spanning animation and robotics. Recently, application of diffusion models for motion generation has enabled improvements in the quality of generated motions. However, existing approaches are limited by their reliance on relatively small-scale motion capture data, leading to poor performance on more diverse, in-the-wild prompts. In this paper, we introduce Make-An-Animation, a text-conditioned human motion generation model which learns more diverse poses and prompts from large-scale image-text datasets, enabling significant improvement in performance over prior works. Make-An-Animation is trained in two stages. First, we train on a curated large-scale dataset of (text, static pseudo-pose) pairs extracted from image-text datasets. Second, we fine-tune on motion capture data, adding additional layers to model the temporal dimension. Unlike prior diffusion models for motion generation, Make-An-Animation uses a U-Net architecture similar to recent text-to-video generation models. Human evaluation of motion realism and alignment with input text shows that our model reaches state-of-the-art performance on text-to-motion generation.

Feed-forward 3D generative models like the Large Reconstruction Model (LRM) have demonstrated exceptional generation speed. However, the transformer-based methods do not leverage the geometric priors of the triplane component in their architecture, often leading to sub-optimal quality given the limited size of 3D data and slow training. In this work, we present the Convolutional Reconstruction Model (CRM), a high-fidelity feed-forward single image-to-3D generative model. Recognizing the limitations posed by sparse 3D data, we highlight the necessity of integrating geometric priors into network design. CRM builds on the key observation that the visualization of triplane exhibits spatial correspondence of six orthographic images. First, it generates six orthographic view images from a single input image, then feeds these images into a convolutional U-Net, leveraging its strong pixel-level alignment capabilities and significant bandwidth to create a high-resolution triplane. CRM further employs Flexicubes as geometric representation, facilitating direct end-to-end optimization on textured meshes. Overall, our model delivers a high-fidelity textured mesh from an image in just 10 seconds, without any test-time optimization.

It is highly desirable to obtain a model that can generate high-quality 3D meshes from text prompts in just seconds. While recent attempts have adapted pre-trained text-to-image diffusion models, such as Stable Diffusion (SD), into generators of 3D representations (e.g., Triplane), they often suffer from poor quality due to the lack of sufficient high-quality 3D training data. Aiming at overcoming the data shortage, we propose a novel training scheme, termed as Progressive Rendering Distillation (PRD), eliminating the need for 3D ground-truths by distilling multi-view diffusion models and adapting SD into a native 3D generator. In each iteration of training, PRD uses the U-Net to progressively denoise the latent from random noise for a few steps, and in each step it decodes the denoised latent into 3D output. Multi-view diffusion models, including MVDream and RichDreamer, are used in joint with SD to distill text-consistent textures and geometries into the 3D outputs through score distillation. Since PRD supports training without 3D ground-truths, we can easily scale up the training data and improve generation quality for challenging text prompts with creative concepts. Meanwhile, PRD can accelerate the inference speed of the generation model in just a few steps. With PRD, we train a Triplane generator, namely TriplaneTurbo, which adds only 2.5% trainable parameters to adapt SD for Triplane generation. TriplaneTurbo outperforms previous text-to-3D generators in both efficiency and quality. Specifically, it can produce high-quality 3D meshes in 1.2 seconds and generalize well for challenging text input. The code is available at https://github.com/theEricMa/TriplaneTurbo.

Modern text-to-video synthesis models demonstrate coherent, photorealistic generation of complex videos from a text description. However, most existing models lack fine-grained control over camera movement, which is critical for downstream applications related to content creation, visual effects, and 3D vision. Recently, new methods demonstrate the ability to generate videos with controllable camera poses these techniques leverage pre-trained U-Net-based diffusion models that explicitly disentangle spatial and temporal generation. Still, no existing approach enables camera control for new, transformer-based video diffusion models that process spatial and temporal information jointly. Here, we propose to tame video transformers for 3D camera control using a ControlNet-like conditioning mechanism that incorporates spatiotemporal camera embeddings based on Plucker coordinates. The approach demonstrates state-of-the-art performance for controllable video generation after fine-tuning on the RealEstate10K dataset. To the best of our knowledge, our work is the first to enable camera control for transformer-based video diffusion models.

Meningiomas are the most common type of primary brain tumor, accounting for approximately 30% of all brain tumors. A substantial number of these tumors are never surgically removed but rather monitored over time. Automatic and precise meningioma segmentation is therefore beneficial to enable reliable growth estimation and patient-specific treatment planning. In this study, we propose the inclusion of attention mechanisms over a U-Net architecture: (i) Attention-gated U-Net (AGUNet) and (ii) Dual Attention U-Net (DAUNet), using a 3D MRI volume as input. Attention has the potential to leverage the global context and identify features' relationships across the entire volume. To limit spatial resolution degradation and loss of detail inherent to encoder-decoder architectures, we studied the impact of multi-scale input and deep supervision components. The proposed architectures are trainable end-to-end and each concept can be seamlessly disabled for ablation studies. The validation studies were performed using a 5-fold cross validation over 600 T1-weighted MRI volumes from St. Olavs University Hospital, Trondheim, Norway. For the best performing architecture, an average Dice score of 81.6% was reached for an F1-score of 95.6%. With an almost perfect precision of 98%, meningiomas smaller than 3ml were occasionally missed hence reaching an overall recall of 93%. Leveraging global context from a 3D MRI volume provided the best performances, even if the native volume resolution could not be processed directly. Overall, near-perfect detection was achieved for meningiomas larger than 3ml which is relevant for clinical use. In the future, the use of multi-scale designs and refinement networks should be further investigated to improve the performance. A larger number of cases with meningiomas below 3ml might also be needed to improve the performance for the smallest tumors.

We propose a novel point cloud U-Net diffusion architecture for 3D generative modeling capable of generating high-quality and diverse 3D shapes while maintaining fast generation times. Our network employs a dual-branch architecture, combining the high-resolution representations of points with the computational efficiency of sparse voxels. Our fastest variant outperforms all non-diffusion generative approaches on unconditional shape generation, the most popular benchmark for evaluating point cloud generative models, while our largest model achieves state-of-the-art results among diffusion methods, with a runtime approximately 70% of the previously state-of-the-art PVD. Beyond unconditional generation, we perform extensive evaluations, including conditional generation on all categories of ShapeNet, demonstrating the scalability of our model to larger datasets, and implicit generation which allows our network to produce high quality point clouds on fewer timesteps, further decreasing the generation time. Finally, we evaluate the architecture's performance in point cloud completion and super-resolution. Our model excels in all tasks, establishing it as a state-of-the-art diffusion U-Net for point cloud generative modeling. The code is publicly available at https://github.com/JohnRomanelis/SPVD.git.

Blood vessels of the brain provide the human brain with the required nutrients and oxygen. As a vulnerable part of the cerebral blood supply, pathology of small vessels can cause serious problems such as Cerebral Small Vessel Diseases (CSVD). It has also been shown that CSVD is related to neurodegeneration, such as Alzheimer's disease. With the advancement of 7 Tesla MRI systems, higher spatial image resolution can be achieved, enabling the depiction of very small vessels in the brain. Non-Deep Learning-based approaches for vessel segmentation, e.g., Frangi's vessel enhancement with subsequent thresholding, are capable of segmenting medium to large vessels but often fail to segment small vessels. The sensitivity of these methods to small vessels can be increased by extensive parameter tuning or by manual corrections, albeit making them time-consuming, laborious, and not feasible for larger datasets. This paper proposes a deep learning architecture to automatically segment small vessels in 7 Tesla 3D Time-of-Flight (ToF) Magnetic Resonance Angiography (MRA) data. The algorithm was trained and evaluated on a small imperfect semi-automatically segmented dataset of only 11 subjects; using six for training, two for validation, and three for testing. The deep learning model based on U-Net Multi-Scale Supervision was trained using the training subset and was made equivariant to elastic deformations in a self-supervised manner using deformation-aware learning to improve the generalisation performance. The proposed technique was evaluated quantitatively and qualitatively against the test set and achieved a Dice score of 80.44 pm 0.83. Furthermore, the result of the proposed method was compared against a selected manually segmented region (62.07 resultant Dice) and has shown a considerable improvement (18.98\%) with deformation-aware learning.

Vision transformers are effective deep learning models for vision tasks, including medical image segmentation. However, they lack efficiency and translational invariance, unlike convolutional neural networks (CNNs). To model long-range interactions in 3D brain lesion segmentation, we propose an all-convolutional transformer block variant of the U-Net architecture. We demonstrate that our model provides the greatest compromise in three factors: performance competitive with the state-of-the-art; parameter efficiency of a CNN; and the favourable inductive biases of a transformer. Our public implementation is available at https://github.com/liamchalcroft/MDUNet .

We present a 3D scene completion method that recovers the complete geometry of multiple unseen objects in complex scenes from a single RGB-D image. Despite notable advancements in single-object 3D shape completion, high-quality reconstructions in highly cluttered real-world multi-object scenes remains a challenge. To address this issue, we propose OctMAE, an architecture that leverages an Octree U-Net and a latent 3D MAE to achieve high-quality and near real-time multi-object scene completion through both local and global geometric reasoning. Because a naive 3D MAE can be computationally intractable and memory intensive even in the latent space, we introduce a novel occlusion masking strategy and adopt 3D rotary embeddings, which significantly improves the runtime and scene completion quality. To generalize to a wide range of objects in diverse scenes, we create a large-scale photorealistic dataset, featuring a diverse set of 12K 3D object models from the Objaverse dataset which are rendered in multi-object scenes with physics-based positioning. Our method outperforms the current state-of-the-art on both synthetic and real-world datasets and demonstrates a strong zero-shot capability.

Speech-driven 3D facial animation is challenging due to the scarcity of large-scale visual-audio datasets despite extensive research. Most prior works, typically focused on learning regression models on a small dataset using the method of least squares, encounter difficulties generating diverse lip movements from speech and require substantial effort in refining the generated outputs. To address these issues, we propose a speech-driven 3D facial animation with a diffusion model (SAiD), a lightweight Transformer-based U-Net with a cross-modality alignment bias between audio and visual to enhance lip synchronization. Moreover, we introduce BlendVOCA, a benchmark dataset of pairs of speech audio and parameters of a blendshape facial model, to address the scarcity of public resources. Our experimental results demonstrate that the proposed approach achieves comparable or superior performance in lip synchronization to baselines, ensures more diverse lip movements, and streamlines the animation editing process.

The practicality of 3D object pose estimation remains limited for many applications due to the need for prior knowledge of a 3D model and a training period for new objects. To address this limitation, we propose an approach that takes a single image of a new object as input and predicts the relative pose of this object in new images without prior knowledge of the object's 3D model and without requiring training time for new objects and categories. We achieve this by training a model to directly predict discriminative embeddings for viewpoints surrounding the object. This prediction is done using a simple U-Net architecture with attention and conditioned on the desired pose, which yields extremely fast inference. We compare our approach to state-of-the-art methods and show it outperforms them both in terms of accuracy and robustness. Our source code is publicly available at https://github.com/nv-nguyen/nope

We present VoloGAN, an adversarial domain adaptation network that translates synthetic RGB-D images of a high-quality 3D model of a person, into RGB-D images that could be generated with a consumer depth sensor. This system is especially useful to generate high amount training data for single-view 3D reconstruction algorithms replicating the real-world capture conditions, being able to imitate the style of different sensor types, for the same high-end 3D model database. The network uses a CycleGAN framework with a U-Net architecture for the generator and a discriminator inspired by SIV-GAN. We use different optimizers and learning rate schedules to train the generator and the discriminator. We further construct a loss function that considers image channels individually and, among other metrics, evaluates the structural similarity. We demonstrate that CycleGANs can be used to apply adversarial domain adaptation of synthetic 3D data to train a volumetric video generator model having only few training samples.

Radio frequency (RF) signal mapping, which is the process of analyzing and predicting the RF signal strength and distribution across specific areas, is crucial for cellular network planning and deployment. Traditional approaches to RF signal mapping rely on statistical models constructed based on measurement data, which offer low complexity but often lack accuracy, or ray tracing tools, which provide enhanced precision for the target area but suffer from increased computational complexity. Recently, machine learning (ML) has emerged as a data-driven method for modeling RF signal propagation, which leverages models trained on synthetic datasets to perform RF signal mapping in "unseen" areas. In this paper, we present Geo2SigMap, an ML-based framework for efficient and high-fidelity RF signal mapping using geographic databases. First, we develop an automated framework that seamlessly integrates three open-source tools: OpenStreetMap (geographic databases), Blender (computer graphics), and Sionna (ray tracing), enabling the efficient generation of large-scale 3D building maps and ray tracing models. Second, we propose a cascaded U-Net model, which is pre-trained on synthetic datasets and employed to generate detailed RF signal maps, leveraging environmental information and sparse measurement data. Finally, we evaluate the performance of Geo2SigMap via a real-world measurement campaign, where three types of user equipment (UE) collect over 45,000 data points related to cellular information from six LTE cells operating in the citizens broadband radio service (CBRS) band. Our results show that Geo2SigMap achieves an average root-mean-square-error (RMSE) of 6.04 dB for predicting the reference signal received power (RSRP) at the UE, representing an average RMSE improvement of 3.59 dB compared to existing methods.

Semantic segmentation of brain tumors is a fundamental medical image analysis task involving multiple MRI imaging modalities that can assist clinicians in diagnosing the patient and successively studying the progression of the malignant entity. In recent years, Fully Convolutional Neural Networks (FCNNs) approaches have become the de facto standard for 3D medical image segmentation. The popular "U-shaped" network architecture has achieved state-of-the-art performance benchmarks on different 2D and 3D semantic segmentation tasks and across various imaging modalities. However, due to the limited kernel size of convolution layers in FCNNs, their performance of modeling long-range information is sub-optimal, and this can lead to deficiencies in the segmentation of tumors with variable sizes. On the other hand, transformer models have demonstrated excellent capabilities in capturing such long-range information in multiple domains, including natural language processing and computer vision. Inspired by the success of vision transformers and their variants, we propose a novel segmentation model termed Swin UNEt TRansformers (Swin UNETR). Specifically, the task of 3D brain tumor semantic segmentation is reformulated as a sequence to sequence prediction problem wherein multi-modal input data is projected into a 1D sequence of embedding and used as an input to a hierarchical Swin transformer as the encoder. The swin transformer encoder extracts features at five different resolutions by utilizing shifted windows for computing self-attention and is connected to an FCNN-based decoder at each resolution via skip connections. We have participated in BraTS 2021 segmentation challenge, and our proposed model ranks among the top-performing approaches in the validation phase. Code: https://monai.io/research/swin-unetr

With the rapid evolution of 3D generation algorithms, the cost of producing 3D humanoid character models has plummeted, yet the field is impeded by the lack of a comprehensive dataset for automatic rigging, which is a pivotal step in character animation. Addressing this gap, we present HumanRig, the first large-scale dataset specifically designed for 3D humanoid character rigging, encompassing 11,434 meticulously curated T-posed meshes adhered to a uniform skeleton topology. Capitalizing on this dataset, we introduce an innovative, data-driven automatic rigging framework, which overcomes the limitations of GNN-based methods in handling complex AI-generated meshes. Our approach integrates a Prior-Guided Skeleton Estimator (PGSE) module, which uses 2D skeleton joints to provide a preliminary 3D skeleton, and a Mesh-Skeleton Mutual Attention Network (MSMAN) that fuses skeleton features with 3D mesh features extracted by a U-shaped point transformer. This enables a coarse-to-fine 3D skeleton joint regression and a robust skinning estimation, surpassing previous methods in quality and versatility. This work not only remedies the dataset deficiency in rigging research but also propels the animation industry towards more efficient and automated character rigging pipelines.

In this study, we aim to build up a model that can Segment Anything in radiology scans, driven by medical terminologies as Text prompts, termed as SAT. Our main contributions are three folds: (i) for dataset construction, we construct the first multi-modal knowledge tree on human anatomy, including 6502 anatomical terminologies; Then, we build up the largest and most comprehensive segmentation dataset for training, by collecting over 22K 3D medical image scans from72 segmentation datasets, across 497 classes, with careful standardization on both image scans and label space; (ii) for architecture design, we propose to inject medical knowledge into a text encoder via contrastive learning, and then formulate a universal segmentation model, that can be prompted by feeding in medical terminologies in text form; (iii) As a result, we have trained SAT-Nano (110M parameters) and SAT-Pro (447M parameters), demonstrating superior or comparable performance to 72 specialist models, i.e., nnU-Nets, U-Mamba or SwinUNETR, trained on each dataset/subsets. We validate SAT as a foundational segmentation model, with better generalization on external (cross-center) datasets, and can be further improved on specific tasks after fine-tuning adaptation. Comparing with state-of-the-art interactive segmentation model MedSAM, SAT demonstrate superior performance, scalability and robustness. We further compare SAT with BiomedParse, and observe SAT is significantly superior in both internal and external evaluation. Through extensive ablation study, we validate the benefit of domain knowledge on universal segmentation, especially on tail categories. As a use case, we demonstrate that SAT can act as a powerful out-of-the-box agent for large language models, enabling visual grounding in versatile application scenarios. All the data, codes, and models in this work have been released.

We present an end-to-end deep learning segmentation method by combining a 3D UNet architecture with a graph neural network (GNN) model. In this approach, the convolutional layers at the deepest level of the UNet are replaced by a GNN-based module with a series of graph convolutions. The dense feature maps at this level are transformed into a graph input to the GNN module. The incorporation of graph convolutions in the UNet provides nodes in the graph with information that is based on node connectivity, in addition to the local features learnt through the downsampled paths. This information can help improve segmentation decisions. By stacking several graph convolution layers, the nodes can access higher order neighbourhood information without substantial increase in computational expense. We propose two types of node connectivity in the graph adjacency: i) one predefined and based on a regular node neighbourhood, and ii) one dynamically computed during training and using the nearest neighbour nodes in the feature space. We have applied this method to the task of segmenting the airway tree from chest CT scans. Experiments have been performed on 32 CTs from the Danish Lung Cancer Screening Trial dataset. We evaluate the performance of the UNet-GNN models with two types of graph adjacency and compare it with the baseline UNet.

Magnetic resonance imaging (MRI) provides high spatial resolution and excellent soft-tissue contrast without using harmful ionising radiation. Dynamic MRI is an essential tool for interventions to visualise movements or changes of the target organ. However, such MRI acquisition with high temporal resolution suffers from limited spatial resolution - also known as the spatio-temporal trade-off of dynamic MRI. Several approaches, including deep learning based super-resolution approaches, have been proposed to mitigate this trade-off. Nevertheless, such an approach typically aims to super-resolve each time-point separately, treating them as individual volumes. This research addresses the problem by creating a deep learning model which attempts to learn both spatial and temporal relationships. A modified 3D UNet model, DDoS-UNet, is proposed - which takes the low-resolution volume of the current time-point along with a prior image volume. Initially, the network is supplied with a static high-resolution planning scan as the prior image along with the low-resolution input to super-resolve the first time-point. Then it continues step-wise by using the super-resolved time-points as the prior image while super-resolving the subsequent time-points. The model performance was tested with 3D dynamic data that was undersampled to different in-plane levels. The proposed network achieved an average SSIM value of 0.951pm0.017 while reconstructing the lowest resolution data (i.e. only 4\% of the k-space acquired) - which could result in a theoretical acceleration factor of 25. The proposed approach can be used to reduce the required scan-time while achieving high spatial resolution.

MonoScene proposes a 3D Semantic Scene Completion (SSC) framework, where the dense geometry and semantics of a scene are inferred from a single monocular RGB image. Different from the SSC literature, relying on 2.5 or 3D input, we solve the complex problem of 2D to 3D scene reconstruction while jointly inferring its semantics. Our framework relies on successive 2D and 3D UNets bridged by a novel 2D-3D features projection inspiring from optics and introduces a 3D context relation prior to enforce spatio-semantic consistency. Along with architectural contributions, we introduce novel global scene and local frustums losses. Experiments show we outperform the literature on all metrics and datasets while hallucinating plausible scenery even beyond the camera field of view. Our code and trained models are available at https://github.com/cv-rits/MonoScene.

The goal of conditional image-to-video (cI2V) generation is to create a believable new video by beginning with the condition, i.e., one image and text.The previous cI2V generation methods conventionally perform in RGB pixel space, with limitations in modeling motion consistency and visual continuity. Additionally, the efficiency of generating videos in pixel space is quite low.In this paper, we propose a novel approach to address these challenges by disentangling the target RGB pixels into two distinct components: spatial content and temporal motions. Specifically, we predict temporal motions which include motion vector and residual based on a 3D-UNet diffusion model. By explicitly modeling temporal motions and warping them to the starting image, we improve the temporal consistency of generated videos. This results in a reduction of spatial redundancy, emphasizing temporal details. Our proposed method achieves performance improvements by disentangling content and motion, all without introducing new structural complexities to the model. Extensive experiments on various datasets confirm our approach's superior performance over the majority of state-of-the-art methods in both effectiveness and efficiency.

The field of controllable human-centric video generation has witnessed remarkable progress, particularly with the advent of diffusion models. However, achieving precise and localized control over human motion in videos, such as replacing or inserting individuals while preserving desired motion patterns, still remains a formidable challenge. In this work, we present the ReplaceAnyone framework, which focuses on localized human replacement and insertion featuring intricate backgrounds. Specifically, we formulate this task as an image-conditioned video inpainting paradigm with pose guidance, utilizing a unified end-to-end video diffusion architecture that facilitates image-conditioned video inpainting within masked regions. To prevent shape leakage and enable granular local control, we introduce diverse mask forms involving both regular and irregular shapes. Furthermore, we implement an enriched visual guidance mechanism to enhance appearance alignment, a hybrid inpainting encoder to further preserve the detailed background information in the masked video, and a two-phase optimization methodology to simplify the training difficulty. ReplaceAnyone enables seamless replacement or insertion of characters while maintaining the desired pose motion and reference appearance within a single framework. Extensive experimental results demonstrate the effectiveness of our method in generating realistic and coherent video content. The proposed ReplaceAnyone can be seamlessly applied not only to traditional 3D-UNet base models but also to DiT-based video models such as Wan2.1. The code will be available at https://github.com/ali-vilab/UniAnimate-DiT.

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.

Recent advances in text-to-video generation have demonstrated the utility of powerful diffusion models. Nevertheless, the problem is not trivial when shaping diffusion models to animate static image (i.e., image-to-video generation). The difficulty originates from the aspect that the diffusion process of subsequent animated frames should not only preserve the faithful alignment with the given image but also pursue temporal coherence among adjacent frames. To alleviate this, we present TRIP, a new recipe of image-to-video diffusion paradigm that pivots on image noise prior derived from static image to jointly trigger inter-frame relational reasoning and ease the coherent temporal modeling via temporal residual learning. Technically, the image noise prior is first attained through one-step backward diffusion process based on both static image and noised video latent codes. Next, TRIP executes a residual-like dual-path scheme for noise prediction: 1) a shortcut path that directly takes image noise prior as the reference noise of each frame to amplify the alignment between the first frame and subsequent frames; 2) a residual path that employs 3D-UNet over noised video and static image latent codes to enable inter-frame relational reasoning, thereby easing the learning of the residual noise for each frame. Furthermore, both reference and residual noise of each frame are dynamically merged via attention mechanism for final video generation. Extensive experiments on WebVid-10M, DTDB and MSR-VTT datasets demonstrate the effectiveness of our TRIP for image-to-video generation. Please see our project page at https://trip-i2v.github.io/TRIP/.

Conditional image-to-video (cI2V) generation aims to synthesize a new plausible video starting from an image (e.g., a person's face) and a condition (e.g., an action class label like smile). The key challenge of the cI2V task lies in the simultaneous generation of realistic spatial appearance and temporal dynamics corresponding to the given image and condition. In this paper, we propose an approach for cI2V using novel latent flow diffusion models (LFDM) that synthesize an optical flow sequence in the latent space based on the given condition to warp the given image. Compared to previous direct-synthesis-based works, our proposed LFDM can better synthesize spatial details and temporal motion by fully utilizing the spatial content of the given image and warping it in the latent space according to the generated temporally-coherent flow. The training of LFDM consists of two separate stages: (1) an unsupervised learning stage to train a latent flow auto-encoder for spatial content generation, including a flow predictor to estimate latent flow between pairs of video frames, and (2) a conditional learning stage to train a 3D-UNet-based diffusion model (DM) for temporal latent flow generation. Unlike previous DMs operating in pixel space or latent feature space that couples spatial and temporal information, the DM in our LFDM only needs to learn a low-dimensional latent flow space for motion generation, thus being more computationally efficient. We conduct comprehensive experiments on multiple datasets, where LFDM consistently outperforms prior arts. Furthermore, we show that LFDM can be easily adapted to new domains by simply finetuning the image decoder. Our code is available at https://github.com/nihaomiao/CVPR23_LFDM.

For many segmentation tasks, especially for the biomedical image, the topological prior is vital information which is useful to exploit. The containment/nesting is a typical inter-class geometric relationship. In the MICCAI Brain tumor segmentation challenge, with its three hierarchically nested classes 'whole tumor', 'tumor core', 'active tumor', the nested classes relationship is introduced into the 3D-residual-Unet architecture. The network comprises a context aggregation pathway and a localization pathway, which encodes increasingly abstract representation of the input as going deeper into the network, and then recombines these representations with shallower features to precisely localize the interest domain via a localization path. The nested-class-prior is combined by proposing the multi-class activation function and its corresponding loss function. The model is trained on the training dataset of Brats2018, and 20% of the dataset is regarded as the validation dataset to determine parameters. When the parameters are fixed, we retrain the model on the whole training dataset. The performance achieved on the validation leaderboard is 86%, 77% and 72% Dice scores for the whole tumor, enhancing tumor and tumor core classes without relying on ensembles or complicated post-processing steps. Based on the same start-of-the-art network architecture, the accuracy of nested-class (enhancing tumor) is reasonably improved from 69% to 72% compared with the traditional Softmax-based method which blind to topological prior.

Convolutional Neural Networks (CNNs) and Vision Transformers (ViT) have been pivotal in biomedical image segmentation, yet their ability to manage long-range dependencies remains constrained by inherent locality and computational overhead. To overcome these challenges, in this technical report, we first propose xLSTM-UNet, a UNet structured deep learning neural network that leverages Vision-LSTM (xLSTM) as its backbone for medical image segmentation. xLSTM is a recently proposed as the successor of Long Short-Term Memory (LSTM) networks and have demonstrated superior performance compared to Transformers and State Space Models (SSMs) like Mamba in Neural Language Processing (NLP) and image classification (as demonstrated in Vision-LSTM, or ViL implementation). Here, xLSTM-UNet we designed extend the success in biomedical image segmentation domain. By integrating the local feature extraction strengths of convolutional layers with the long-range dependency capturing abilities of xLSTM, xLSTM-UNet offers a robust solution for comprehensive image analysis. We validate the efficacy of xLSTM-UNet through experiments. Our findings demonstrate that xLSTM-UNet consistently surpasses the performance of leading CNN-based, Transformer-based, and Mamba-based segmentation networks in multiple datasets in biomedical segmentation including organs in abdomen MRI, instruments in endoscopic images, and cells in microscopic images. With comprehensive experiments performed, this technical report highlights the potential of xLSTM-based architectures in advancing biomedical image analysis in both 2D and 3D. The code, models, and datasets are publicly available at http://tianrun-chen.github.io/xLSTM-UNet/{http://tianrun-chen.github.io/xLSTM-Unet/}

UNet and its variants have been widely used in medical image segmentation. However, these models, especially those based on Transformer architectures, pose challenges due to their large number of parameters and computational loads, making them unsuitable for mobile health applications. Recently, State Space Models (SSMs), exemplified by Mamba, have emerged as competitive alternatives to CNN and Transformer architectures. Building upon this, we employ Mamba as a lightweight substitute for CNN and Transformer within UNet, aiming at tackling challenges stemming from computational resource limitations in real medical settings. To this end, we introduce the Lightweight Mamba UNet (LightM-UNet) that integrates Mamba and UNet in a lightweight framework. Specifically, LightM-UNet leverages the Residual Vision Mamba Layer in a pure Mamba fashion to extract deep semantic features and model long-range spatial dependencies, with linear computational complexity. Extensive experiments conducted on two real-world 2D/3D datasets demonstrate that LightM-UNet surpasses existing state-of-the-art literature. Notably, when compared to the renowned nnU-Net, LightM-UNet achieves superior segmentation performance while drastically reducing parameter and computation costs by 116x and 21x, respectively. This highlights the potential of Mamba in facilitating model lightweighting. Our code implementation is publicly available at https://github.com/MrBlankness/LightM-UNet.

Liver cancer is one of the leading causes of cancer death. To assist doctors in hepatocellular carcinoma diagnosis and treatment planning, an accurate and automatic liver and tumor segmentation method is highly demanded in the clinical practice. Recently, fully convolutional neural networks (FCNs), including 2D and 3D FCNs, serve as the back-bone in many volumetric image segmentation. However, 2D convolutions can not fully leverage the spatial information along the third dimension while 3D convolutions suffer from high computational cost and GPU memory consumption. To address these issues, we propose a novel hybrid densely connected UNet (H-DenseUNet), which consists of a 2D DenseUNet for efficiently extracting intra-slice features and a 3D counterpart for hierarchically aggregating volumetric contexts under the spirit of the auto-context algorithm for liver and tumor segmentation. We formulate the learning process of H-DenseUNet in an end-to-end manner, where the intra-slice representations and inter-slice features can be jointly optimized through a hybrid feature fusion (HFF) layer. We extensively evaluated our method on the dataset of MICCAI 2017 Liver Tumor Segmentation (LiTS) Challenge and 3DIRCADb Dataset. Our method outperformed other state-of-the-arts on the segmentation results of tumors and achieved very competitive performance for liver segmentation even with a single model.

This paper reports Deep LOGISMOS approach to 3D tumor segmentation by incorporating boundary information derived from deep contextual learning to LOGISMOS - layered optimal graph image segmentation of multiple objects and surfaces. Accurate and reliable tumor segmentation is essential to tumor growth analysis and treatment selection. A fully convolutional network (FCN), UNet, is first trained using three adjacent 2D patches centered at the tumor, providing contextual UNet segmentation and probability map for each 2D patch. The UNet segmentation is then refined by Gaussian Mixture Model (GMM) and morphological operations. The refined UNet segmentation is used to provide the initial shape boundary to build a segmentation graph. The cost for each node of the graph is determined by the UNet probability maps. Finally, a max-flow algorithm is employed to find the globally optimal solution thus obtaining the final segmentation. For evaluation, we applied the method to pancreatic tumor segmentation on a dataset of 51 CT scans, among which 30 scans were used for training and 21 for testing. With Deep LOGISMOS, DICE Similarity Coefficient (DSC) and Relative Volume Difference (RVD) reached 83.2+-7.8% and 18.6+-17.4% respectively, both are significantly improved (p<0.05) compared with contextual UNet and/or LOGISMOS alone.

We propose a method for generating fly-through videos of a scene, from a single image and a given camera trajectory. We build upon an image-to-video latent diffusion model. We condition its UNet denoiser on the camera trajectory, using four techniques. (1) We condition the UNet's temporal blocks on raw camera extrinsics, similar to MotionCtrl. (2) We use images containing camera rays and directions, similar to CameraCtrl. (3) We reproject the initial image to subsequent frames and use the resulting video as a condition. (4) We use 2D<=>3D transformers to introduce a global 3D representation, which implicitly conditions on the camera poses. We combine all conditions in a ContolNet-style architecture. We then propose a metric that evaluates overall video quality and the ability to preserve details with view changes, which we use to analyze the trade-offs of individual and combined conditions. Finally, we identify an optimal combination of conditions. We calibrate camera positions in our datasets for scale consistency across scenes, and we train our scene exploration model, CamCtrl3D, demonstrating state-of-theart results.

Vision Transformers (ViT)s have shown great performance in self-supervised learning of global and local representations that can be transferred to downstream applications. Inspired by these results, we introduce a novel self-supervised learning framework with tailored proxy tasks for medical image analysis. Specifically, we propose: (i) a new 3D transformer-based model, dubbed Swin UNEt TRansformers (Swin UNETR), with a hierarchical encoder for self-supervised pre-training; (ii) tailored proxy tasks for learning the underlying pattern of human anatomy. We demonstrate successful pre-training of the proposed model on 5,050 publicly available computed tomography (CT) images from various body organs. The effectiveness of our approach is validated by fine-tuning the pre-trained models on the Beyond the Cranial Vault (BTCV) Segmentation Challenge with 13 abdominal organs and segmentation tasks from the Medical Segmentation Decathlon (MSD) dataset. Our model is currently the state-of-the-art (i.e. ranked 1st) on the public test leaderboards of both MSD and BTCV datasets. Code: https://monai.io/research/swin-unetr

Existing methodologies in open vocabulary 3D semantic segmentation primarily concentrate on establishing a unified feature space encompassing 3D, 2D, and textual modalities. Nevertheless, traditional techniques such as global feature alignment or vision-language model distillation tend to impose only approximate correspondence, struggling notably with delineating fine-grained segmentation boundaries. To address this gap, we propose a more meticulous mask-level alignment between 3D features and the 2D-text embedding space through a cross-modal mask reasoning framework, XMask3D. In our approach, we developed a mask generator based on the denoising UNet from a pre-trained diffusion model, leveraging its capability for precise textual control over dense pixel representations and enhancing the open-world adaptability of the generated masks. We further integrate 3D global features as implicit conditions into the pre-trained 2D denoising UNet, enabling the generation of segmentation masks with additional 3D geometry awareness. Subsequently, the generated 2D masks are employed to align mask-level 3D representations with the vision-language feature space, thereby augmenting the open vocabulary capability of 3D geometry embeddings. Finally, we fuse complementary 2D and 3D mask features, resulting in competitive performance across multiple benchmarks for 3D open vocabulary semantic segmentation. Code is available at https://github.com/wangzy22/XMask3D.

Analysis of 3D segmentation models, especially in the context of medical imaging, is often limited to segmentation performance metrics that overlook the crucial aspect of explainability and bias. Currently, effectively explaining these models with saliency maps is challenging due to the high dimensions of input images multiplied by the ever-growing number of segmented class labels. To this end, we introduce Agg^2Exp, a methodology for aggregating fine-grained voxel attributions of the segmentation model's predictions. Unlike classical explanation methods that primarily focus on the local feature attribution, Agg^2Exp enables a more comprehensive global view on the importance of predicted segments in 3D images. Our benchmarking experiments show that gradient-based voxel attributions are more faithful to the model's predictions than perturbation-based explanations. As a concrete use-case, we apply Agg^2Exp to discover knowledge acquired by the Swin UNEt TRansformer model trained on the TotalSegmentator v2 dataset for segmenting anatomical structures in computed tomography medical images. Agg^2Exp facilitates the explanatory analysis of large segmentation models beyond their predictive performance.

This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. The results of comparative assessments indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines, airways, and vascular structures. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.

Recent advances in Vision Transformers (ViTs) have significantly enhanced medical image segmentation by facilitating the learning of global relationships. However, these methods face a notable challenge in capturing diverse local and global long-range sequential feature representations, particularly evident in whole-body CT (WBCT) scans. To overcome this limitation, we introduce Swin Soft Mixture Transformer (Swin SMT), a novel architecture based on Swin UNETR. This model incorporates a Soft Mixture-of-Experts (Soft MoE) to effectively handle complex and diverse long-range dependencies. The use of Soft MoE allows for scaling up model parameters maintaining a balance between computational complexity and segmentation performance in both training and inference modes. We evaluate Swin SMT on the publicly available TotalSegmentator-V2 dataset, which includes 117 major anatomical structures in WBCT images. Comprehensive experimental results demonstrate that Swin SMT outperforms several state-of-the-art methods in 3D anatomical structure segmentation, achieving an average Dice Similarity Coefficient of 85.09%. The code and pre-trained weights of Swin SMT are publicly available at https://github.com/MI2DataLab/SwinSMT.

In medical imaging, the primary challenge is collecting large-scale labeled data due to privacy concerns, logistics, and high labeling costs. In this work, we present the UK Biobank Organs and Bones (UKBOB), the largest labeled dataset of body organs, comprising 51,761 MRI 3D samples (equivalent to 17.9 million 2D images) and more than 1.37 billion 2D segmentation masks of 72 organs, all based on the UK Biobank MRI dataset. We utilize automatic labeling, introduce an automated label cleaning pipeline with organ-specific filters, and manually annotate a subset of 300 MRIs with 11 abdominal classes to validate the quality (referred to as UKBOB-manual). This approach allows for scaling up the dataset collection while maintaining confidence in the labels. We further confirm the validity of the labels by demonstrating zero-shot generalization of trained models on the filtered UKBOB to other small labeled datasets from similar domains (e.g., abdominal MRI). To further mitigate the effect of noisy labels, we propose a novel method called Entropy Test-time Adaptation (ETTA) to refine the segmentation output. We use UKBOB to train a foundation model, Swin-BOB, for 3D medical image segmentation based on the Swin-UNetr architecture, achieving state-of-the-art results in several benchmarks in 3D medical imaging, including the BRATS brain MRI tumor challenge (with a 0.4% improvement) and the BTCV abdominal CT scan benchmark (with a 1.3% improvement). The pre-trained models and the code are available at https://emmanuelleb985.github.io/ukbob , and the filtered labels will be made available with the UK Biobank.

Longitudinal analysis has great potential to reveal developmental trajectories and monitor disease progression in medical imaging. This process relies on consistent and robust joint 4D segmentation. Traditional techniques are dependent on the similarity of images over time and the use of subject-specific priors to reduce random variation and improve the robustness and sensitivity of the overall longitudinal analysis. This is however slow and computationally intensive as subject-specific templates need to be rebuilt every time. The focus of this work to accelerate this analysis with the use of deep learning. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The state of art using 3D patches as inputs to modified Unet provides results around {0.91 pm 0.5} Dice and using multi-view atlas in CNNs provide around the same results. In this work, different models are explored, each offers better accuracy and fast results while increasing the segmentation quality. These methods are evaluated on 135 scans from the EADC-ADNI Harmonized Hippocampus Protocol. Proposed CNN based segmentation approaches demonstrate how 2D segmentation using prior slices can provide similar results to 3D segmentation while maintaining good continuity in the 3D dimension and improved speed. Just using 2D modified sagittal slices provide us a better Dice and longitudinal analysis for a given subject. For the ADNI dataset, using the simple UNet CNN technique gives us {0.84 pm 0.5} and while using modified CNN techniques on the same input yields {0.89 pm 0.5}. Rate of atrophy and RMS error are calculated for several test cases using various methods and analyzed.

Automatic identification of brain lesions from magnetic resonance imaging (MRI) scans of stroke survivors would be a useful aid in patient diagnosis and treatment planning. We propose a multi-modal multi-path convolutional neural network system for automating stroke lesion segmentation. Our system has nine end-to-end UNets that take as input 2-dimensional (2D) slices and examines all three planes with three different normalizations. Outputs from these nine total paths are concatenated into a 3D volume that is then passed to a 3D convolutional neural network to output a final lesion mask. We trained and tested our method on datasets from three sources: Medical College of Wisconsin (MCW), Kessler Foundation (KF), and the publicly available Anatomical Tracings of Lesions After Stroke (ATLAS) dataset. Cross-study validation results (with independent training and validation datasets) were obtained to compare with previous methods based on naive Bayes, random forests, and three recently published convolutional neural networks. Model performance was quantified in terms of the Dice coefficient. Training on the KF and MCW images and testing on the ATLAS images yielded a mean Dice coefficient of 0.54. This was reliably better than the next best previous model, UNet, at 0.47. Reversing the train and test datasets yields a mean Dice of 0.47 on KF and MCW images, whereas the next best UNet reaches 0.45. With all three datasets combined, the current system compared to previous methods also attained a reliably higher cross-validation accuracy. It also achieved high Dice values for many smaller lesions that existing methods have difficulty identifying. Overall, our system is a clear improvement over previous methods for automating stroke lesion segmentation, bringing us an important step closer to the inter-rater accuracy level of human experts.

Sora-like video generation models have achieved remarkable progress with a Multi-Modal Diffusion Transformer MM-DiT architecture. However, the current video generation models predominantly focus on single-prompt, struggling to generate coherent scenes with multiple sequential prompts that better reflect real-world dynamic scenarios. While some pioneering works have explored multi-prompt video generation, they face significant challenges including strict training data requirements, weak prompt following, and unnatural transitions. To address these problems, we propose DiTCtrl, a training-free multi-prompt video generation method under MM-DiT architectures for the first time. Our key idea is to take the multi-prompt video generation task as temporal video editing with smooth transitions. To achieve this goal, we first analyze MM-DiT's attention mechanism, finding that the 3D full attention behaves similarly to that of the cross/self-attention blocks in the UNet-like diffusion models, enabling mask-guided precise semantic control across different prompts with attention sharing for multi-prompt video generation. Based on our careful design, the video generated by DiTCtrl achieves smooth transitions and consistent object motion given multiple sequential prompts without additional training. Besides, we also present MPVBench, a new benchmark specially designed for multi-prompt video generation to evaluate the performance of multi-prompt generation. Extensive experiments demonstrate that our method achieves state-of-the-art performance without additional training.