This repo is now trimmed to the active salamander brightfield workflow:

• Cell segmentation with the custom Cellpose cell model
• Nucleus segmentation with the custom YOLO nucleus model
• Nucleus IOD measurement
• Cell+nucleus linkage with full traceability

The main workflow document is:

• docs/MIXED_CELLPOSE_YOLO_WORKFLOW.md

The active code and artifact inventory is:

• docs/ACTIVE_WORKFLOW_INVENTORY.md

Key active entrypoints:

• cell_size_segmentation_pipeline/run_from_manifest.py
• nucleus_iod_estimate_pipeline/run_from_manifest.py
• scripts/run_yolo_tile_measurements.py
• scripts/build_cell_nucleus_linkage_report.py
• scripts/build_species_linked_stats_report.py
• scripts/run_linked_pair_review.py
• scripts/apply_pair_review_repairs.py

Current full-dataset mixed outputs:

• output/runs/full_dataset_v1
• output/runs/mixed_cellpose_yolo_full_dataset_v1