README.md

czi2png

This wrapper GUI + script (around the aicslibczi library) for batch processing / converting your '.czi' files to '.png's

Info

• Written by: Pete, 2022, (peterlionelnewman)
• Paper doi: doi.org/10.1002/advs.202204741
• Paper url: https://onlinelibrary.wiley.com/doi/10.1002/advs.202204741
• Cite us if you use any part of this script in anyway :-)

1. searches a folder for .czi files
2. exports a mip of each czi channel

To run, use something something like:

    conda create -n czi2png python=3.10.6 pip
    conda activate czi2png
    cd <path to czi2png>
    pip install -r requirements.txt
    python main.py 

• best ran from a conda venv
• see requirements.txt

To use

1. Click and specify the search path button search fo czi's
2. Click and specify the saving path
3. Select options for png export
4. Click 'Converyt 2 png'!

i.e.:

Notes

• Go check out the Allen Institue of Cell Science package !!!
• This exists because sometimes the AICS package is buggy with rounding errors. But otherwise we AOK.