README.md

cziPy for WSI.czi -> png patches.

Using python-bioformats to tile/patch whole slide images in .czi format (for Zeiss WSI scanners)

Basic usage

To run an experiment, while in the root directory of the project, the command:

python cziPy.py --czi_dir "/dir/of/czi/files/" --patch_dir "/dir/target/for/patches/"

To see all possible arguments, run the following:

python cziPy.py --help

Environment setup (tested for ubuntu)

1. Download a copy of the repository

git clone https://github.com/CraigMyles/cziPy

2. cd into cziPy direcory

cd cziPy/

3. Create the environment

make create_environment

4. Install Java

make install_java

5. Activate cziPy environment

conda activate cziPy