This contains the code for our chromosome segmentation tool. The notebook files were for our personal testing and early implemntations.
| File | Description |
|---|---|
| config.ini | Configuration file to set parameters |
| environment.yml | File to create the environment |
| Folder | Description |
|---|---|
| sample | Folder containing sample images to use with our project |
| src | Contains our Python scripts |
To get started, run the following code to create the environment.
git clone
cd ecDNA-Capstone
conda env create -f environment.yml
conda activate cap
Input folder will only read .tif files
- Change the config.ini file to your own file path. If not set, 3 sample images are provided to test output.
- Run chromosome.py
- Annotated images will show up under annotated/filename/a_filename.tif
- output.csv contains info in the format of filename, number of chromosomes