Kidney WSI segmentation of diagnostic tissue compartments

3-stage model

• Tissue segmentation: tree structure
• Instance segmentation: mmdet
• Post-processing step: only in inference stage

Commands for running

Generate data

• QuPath script: how to use groovy file
• Python script: generate json files

Installation and some problems

If you want to generate glom,artery, arteriole on a new collection of WSIs.

Evaluation

The Python generation file also contains evaluation code

Discriminate Qupath scripts and Python scripts for generating labels

Crop vs multi, Pad vs no pad

Trained checkpoints and norm files

Acknowledgement

mmdet library