https://github.com/abailoni/cell-cme

https://github.com/abailoni/cell-cme

Last synced: 24 days ago
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• Host: GitHub
• URL: https://github.com/abailoni/cell-cme
• Owner: abailoni
• Created: 2020-10-26T16:02:34.000Z (about 4 years ago)
• Default Branch: master
• Last Pushed: 2021-03-29T12:49:20.000Z (almost 4 years ago)
• Last Synced: 2024-11-05T11:55:28.195Z (2 months ago)
• Language: Python
• Size: 9.77 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
### Installation

- Clone the repository: `git clone https://github.com/abailoni/cell-CME.git`

- Move to the package directory: `cd cell-CME`

- To install the dependencies, you will need [miniconda](https://docs.conda.io/en/latest/miniconda.html) or [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/)

- Once you have installed conda, run the command  `conda env create --name=cellCME --file=environment.yml`

- Before to run any of the scripts, activate your new environment with `conda activate cellCME`

- Install package with `python setup.py install`  

### Usage

- Data should be organized as follows:

```

ROOT_DATA_DIR:

    input_images:

        Place here the images with .czi or .dv formats (They can also be organized in subdirectories)

    converted_to_tif:

        Converted tif images used by ilastik will be placed here

    converted_to_jpg:

        Converted jpg images will be placed here

    resulting_segmentations:

        Final segmentation images will be placed here

```

- To convert images to tif format (accepted by ilastik):

    - Run `python scripts/convert_input_images.py --ROOT_DATA_DIR=`

    - Images will be found in the `converted_to_tif` and `converted_to_jpg` subfolders

- To train ilastik classifier, see [Wiki page](https://github.com/abailoni/cell-CME/wiki/Training-ilastik-classifier)

- To plot the final segmentations:

    - Run `python scripts/plot_output_segmentation.py --ROOT_DATA_DIR=`

    - Images will be found in the `resulting_segmentations` subfolder

- To be continued...