Orion

Patch-first Orion multiplex imaging pipeline.

Commands

uv run python3 main.py --configuration configurations/CRC33_01.yaml --mode patch
uv run python3 main.py --configuration configurations/CRC33_01.yaml --mode patch --stage segment
uv run python3 main.py --configuration configurations/CRC33_01.yaml --mode whole-slide

patch is the implemented mode. whole-slide is a reserved development flag that currently exits with a clear not-implemented message.