This repository is designed for analysing images of nuclei using deep learning However, it is specialised for analysing 2D max-Z projections of organoids, though it may have general usage outside of this specific task.
This does contains a full snakemake pipeline to:
- Train UNet and *Dist models
- Run inference using models on Cellesce data
- Convert inference images to per-nuclei features
- Compile nuclei into a csv
Add secrets
set -o allexport; source secrets.env;set +o allexport
Install env
make install.snakemake.env
Test Snakemake
snakemake --dry-run
Produce graphs
python splines.py
TODO:
- Get automatic zenodo uploading working
- Seperate the UNet package into it's own git repo
- Add Figures