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1 | 1 | # MyoQuant
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2 | 2 |
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3 |
| -MyoQuant command line tool to quantifying pathological feature in histology images. |
4 |
| -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/). |
| 3 | +MyoQuant is a command line tool to quantify pathological feature in histology images. |
| 4 | +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/). |
5 | 5 |
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6 | 6 | ### **Warning:** This tool is still in alpha stage and might not work perfectly... yet.
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7 | 7 |
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8 | 8 | ## How to install
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9 | 9 |
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10 | 10 | ### Installing from PyPi
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11 | 11 |
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12 |
| -Using pip, you can simply install MyoQuant in a python environnement with a simple: `pip install myoquant` |
| 12 | +Using pip, you can simply install MyoQuant in a python environment with a simple: `pip install myoquant` |
13 | 13 |
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14 | 14 | ### Installing from source
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15 | 15 |
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16 | 16 | 1. Clone this repository using `git clone https://github.com/lambda-science/MyoQuant.git`
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17 |
| -2. Create a virtual environnement by using `python -m venv .venv` |
| 17 | +2. Create a virtual environment by using `python -m venv .venv` |
18 | 18 | 3. Activate the venv by using `source .venv/bin/activate`
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19 | 19 | 4. Install MyoQuant by using `pip install -e .`
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20 | 20 |
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@@ -52,7 +52,7 @@ For SDH Staining analysis, you can download this sample image: [HERE](https://ww
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52 | 52 | - 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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53 | 53 | - The source code for this application is available [HERE](https://github.com/lambda-science/MyoQuant)
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54 | 54 |
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55 |
| -## Advanced informations |
| 55 | +## Advanced information |
56 | 56 |
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57 | 57 | 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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58 | 58 | `myoquant sdh_analysis IMAGE_PATH --model_path /path/to/model.h5`
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