This Github page explains how to use the output of ilastik classification in segmentation .tiff files and obtain disease scores per glomeruli.
Code will be provided to run both in Graphical user Interface (GUI) macros for Image J and headless or commandline for command line interaction some helpful hints to track jobs submissions etc. will be provided.
This assumes that you have a working ilastik classifier.
We provide a link to ours here https://storage.googleapis.com/korstanje-public-data/GlomIDDec2017.ilp
With a link to the Images used to train it