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--- |
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title: DNAI |
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emoji: 🚀 |
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colorFrom: red |
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colorTo: red |
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sdk: docker |
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app_port: 8501 |
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tags: |
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- streamlit |
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pinned: false |
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short_description: DNA Fiber semantic segmentation for replication assessment |
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license: mit |
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--- |
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# DN-AI |
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This is the official repository for DN-AI, an automated tool for measurement of differentiated DNA replication in fluorescence microscopy images. |
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DN-AI offers different solutions for biologists to measure DNA replication in fluorescence microscopy images, without requiring programming skills. See the [Installation](#installation) section for instructions on how to install DN-AI. |
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## Features |
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- **Automated DNA replication measurement**: DN-AI can automatically measure the amount of DNA replication in fluorescence microscopy images. We use a deep learning model to segment the images and measure the amount of DNA replication. |
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- **User-friendly interface**: DN-AI provides a web-based user-friendly interface that allows users to easily upload images and view the results. Both jpeg and tiff images are supported. |
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- **Batch processing**: DN-AI can process multiple images at once, making it easy to analyze large datasets. It also supports comparing ratios between different batches of images. |
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## Installation |
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DN-AI relies on Python. We recommend installing its latest version (3.10 or higher) and using a virtual environment to avoid conflicts with other packages. |
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### Prerequisites |
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Before installing DN-AI, make sure you have the following prerequisites installed: |
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- [Python 3.10 or higher](https://www.python.org/downloads/) |
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- [pip](https://pip.pypa.io/en/stable/installation/) (Python package installer) |
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### Python Package |
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To install DN-AI as a Python package, you can use pip: |
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```bash |
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pip install git+https://github.com/ClementPla/DeepFiberQ.git |
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``` |
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### Graphical User Interface (GUI) |
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To run the DN-AI graphical user interface, you can use the following command: |
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```bash |
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DNAI |
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``` |
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Make sure you are running this command in the terminal where you have installed DN-AI. This will start a local web server and you will see output similar to: |
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Then open your web browser and go to `http://localhost:8501` to access the DN-AI interface. |
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Screenshots of the GUI: |
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### Docker |
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A Docker image is available for DN-AI. You can pull the image from Docker Hub: |
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```bash |
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docker pull clementpla/dnafiber |
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``` |
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### Google Colab |
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We also provide a Google Colab notebook for DN-AI. You can access it [here](https://colab.research.google.com/github/ClementPla/DeepFiberQ/blob/main/Colab/DNA_Fiber_Q.ipynb). |
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