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README.md

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# MyoQuant
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MyoQuant command line tool to quantifying pathological feature in histology images.
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It is built using CellPose, Stardist and custom models and image analysis techniques to automatically analyze myopathy histology images. An online demo with a web interface is availiable at [https://lbgi.fr/MyoQuant/](https://lbgi.fr/MyoQuant/).
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MyoQuant is a command line tool to quantify pathological feature in histology images.
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It is built using CellPose, Stardist, custom neural-network models and image analysis techniques to automatically analyze myopathy histology images. An online demo with a web interface is available at [https://lbgi.fr/MyoQuant/](https://lbgi.fr/MyoQuant/).
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### **Warning:** This tool is still in alpha stage and might not work perfectly... yet.
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## How to install
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### Installing from PyPi
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Using pip, you can simply install MyoQuant in a python environnement with a simple: `pip install myoquant`
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Using pip, you can simply install MyoQuant in a python environment with a simple: `pip install myoquant`
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### Installing from source
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1. Clone this repository using `git clone https://github.com/lambda-science/MyoQuant.git`
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2. Create a virtual environnement by using `python -m venv .venv`
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2. Create a virtual environment by using `python -m venv .venv`
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3. Activate the venv by using `source .venv/bin/activate`
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4. Install MyoQuant by using `pip install -e .`
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- Creator and Maintainer: [Corentin Meyer, 3rd year PhD Student in the CSTB Team, ICube — CNRS — Unistra](https://lambda-science.github.io/)
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- The source code for this application is available [HERE](https://github.com/lambda-science/MyoQuant)
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## Advanced informations
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## Advanced information
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For the SDH Analysis our custom model will be downloaded and placed inside the myoquant package directory. You can also download it manually here: [https://lbgi.fr/~meyer/SDH_models/model.h5](https://lbgi.fr/~meyer/SDH_models/model.h5) and then you can place it in the directory of your choice and provide the path to the model file using:
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`myoquant sdh_analysis IMAGE_PATH --model_path /path/to/model.h5`

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