Multi compartment segmentation is a detectron2 based panoptic segmentation model that is implemented as a pipeline in Digital Slide Archive (DSA) developed and maintained by CMI lab at the University of Florida. This DSA plugin allows users to segment a kidney Whole Slide Image (WSI) into 6 compartments, namely: cortical interstitium, medullary interstitium, non-sclerotic glomerulus, sclerotic glomerulus, tubule, and artery/arteriole.
This DSA plugin allows users to run image analysis jobs through the HistomicsUI by the following steps:
- Create an account at DSA and log in with your credentials.
- Upload a WSI in a folder either unders Collections tab or in your User directory
- Open the image in HistomicsUI by clicking the arrow icon:
- From Analyses tab on the top right in HistomicsUI select: sarderlab/ComPRePS/segmentation/MultiCompartmentSegment
- Populate the fields in the tab that appears on the left side of the page: Select the Base Directory as the directory where your WSI is located and select the Model File from the Collections/models/segmentation_models/Multi_compartment_model with an available pre train model and click Sumbit botton.
- Once the job sucessfuly runs, the segmented compartments will appear on top of the image. You can visuazlie them all or one-by-one by selecting the layers you wish to view from Annotations/Other tab on the right.
Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine by Lucarelli N. et. al.
Sayat Mimar (SWE): [email protected]
Pinaki Sarder (PI): [email protected]