Nov 15, 2023
Renal Multicompartment Segmentation Object Boundaries
- Nicholas Lucarelli1
- 1University of Florida
Protocol Citation: Nicholas Lucarelli 2023. Renal Multicompartment Segmentation Object Boundaries. protocols.io https://dx.doi.org/10.17504/protocols.io.dm6gp35p8vzp/v1
Manuscript citation:
Lucarelli et. al. Kidney 360. December, 2023.
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
Created: November 15, 2023
Last Modified: November 15, 2023
Protocol Integer ID: 90937
Keywords: renal multicompartment segmentation object boundaries boundary description, renal whole slide image, stained renal whole slide image, multicompartment segmentation pipeline, cmilab multicompartment segmentation pipeline for pa, segmentation, pipeline, image
Abstract
Boundary descriptions for segmentations produced by the CMILab multicompartment segmentation pipeline for PAS-stained renal whole slide images.
segmentations.ome.tiff channels
Cortical Interstitium: Defined as the spaces in the renal cortex situated between basement membranes of glomeruli, tubules, and vessels. Does not include perivascular stroma.
Medulla Interstitium: Defined as the spaces in the renal medulla situated between basement membranes of tubules, and vessels. Does not include perivascular stroma.
Non Globally Sclerotic Glomeruli: Outer boundary is defined by the outer boundary of the bowman's capsule. Glomeruli may show signs of sclerosis but are not deemed globally sclerotic.
Globally Sclerotic Glomeruli: Outer boundary is defined by the outer boundary of what would be the bowman's capsule in a healthy glomerulus. Glomeruli are deemed globally sclerotic, and no longer functional.
Tubules: Outer boundary is defined as the outer boundary of the tubular basement membrane. Classification is not specific to tubular segments (i.e. PCT, DCT, TAL, etc.).
Arteries/Arterioles: Outer boundary is defined as the outer boundary of the medial layer of all arteries or arterioles in the sections. Veins and capillaries are not considered.