This repository contains scripts and pipelines useful for generating data for CODEX/H&E overlaying protocols. groovy scripts are for QuPath scripting

All scripts can be found in the scripts/ folder. To use PyVips and OpenSlide backends, ensure that appropriate bin files for these are included in the following structure at the project root:

backends/
├─ openslide/
│  └─ bin/
│     ├─ filename.dll
│     └─ filename.dll
└─ pyvips/
   └─ bin/
      ├─ filename.dll
      └─ filename.dll

Backends can be downloaded at:

• Openslide: https://openslide.org/download/
• PyVips: https://github.com/libvips/libvips/releases