Kidney Functional Tissue Unit (FTU) Segmentation
Nathan Heath Patterson, Jeff Spraggins, Ellie Pingry, Katerina V Djambazova, Melissa Farrow, Raf Van De Plas
Abstract
This protocol explains how to apply a segmentation model to autofluorescence microscopy images to find kidney functional tissue units (FTUs). Currently the model allows for segmentation of glomeruli, proximal tubules, thick ascending limb, distal tubules, and collecting ducts.
Steps
Apply kidney FTU segmentation to autofluorescence images
Configure the segmentation prediction by creating the dataset .yaml file. Add the path to the saved model and images in the configuration file.
Create the python environment needed to run wsimap. See instructions at the wsimap GitHub.
Run the model using the command line from the wsimap directory like so:
python scripts/config/instance-predict-from-config-newmodels-multi.py "/path/to/configuration-file-from-step2.yaml
Collect .geojson segmentations in output folder specified in .yaml file from Step 2. These can be visualized in QuPath.
