Nov 08, 2024
Manual segmentation of histology images
- Lauren Schwartz1,
- Derek Da Kuang1,
- Kate O'Neill1,
- Harley Hernandez1
- 1University of Pennsylvania
- Human BioMolecular Atlas Program (HuBMAP) Method Development CommunityTech. support email: Jeff.spraggins@vanderbilt.edu
Protocol Citation: Lauren Schwartz, Derek Da Kuang, Kate O'Neill, Harley Hernandez 2024. Manual segmentation of histology images. protocols.io https://dx.doi.org/10.17504/protocols.io.ewov1dybpvr2/v1
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
We use this protocol and it's working
Created: November 05, 2024
Last Modified: November 08, 2024
Protocol Integer ID: 111621
Funders Acknowledgement:
NIH
Grant ID: U54HD104392
Abstract
Here we manually segmented histology images to denote functional tissue units, using the QuPath application.
Materials
Pathologist circled the identified functional tissue region(s).
The masked regions were exported as TIFF files. We used the following script to export the mask from QuPath to coordinates in geoJSON format. This script is specific to segmented tissue regions in the Fallopian tube but should be easily adapted to other tissue and regions.
Once we had the mask coordinates in the geoJSON file, we used this script to convert the coordinates from the geoJSON file into a binary mask in aTIFF file. This script is specific to segmented tissue regions in the Fallopian tube but should be easily adapted to other tissue and regions.