Dec 07, 2023

Public workspaceCD8 Cell Density In Substantia Nigra And Cerebral Peduncle Image Analysis

DOI
dx.doi.org/10.17504/protocols.io.5qpvo3roxv4o/v1
  • 1Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK;
  • 2Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20 815, USA;
  • 3Queen Square Brain Bank for Neurological Disorders (QSBB), 1 Wakefield Street, London WC1N 1PJ, UK
Hemanth Ramesh Nelvagal
Open access
DOI: dx.doi.org/10.17504/protocols.io.5qpvo3roxv4o/v1
Protocol Citation: Hemanth Ramesh Nelvagal, Toby J Curless, Zane Jaunmuktane 2023. CD8 Cell Density In Substantia Nigra And Cerebral Peduncle Image Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.5qpvo3roxv4o/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: August 07, 2023
Last Modified: May 31, 2024
Protocol Integer ID: 86040
Keywords: ASAPCRN, Human Brain, Substantia Nigra, Cerebral Peduncle, CD8, Parkinson’s disease, QuPath, NZConnect, Image Analysis, Pathology
Funders Acknowledgement:
The Michael J. Fox Foundation for Parkinson’s Research (MJFF) and the Aligning Science Across Parkinson’s (ASAP) Initiative
Grant ID: ASAP-000478
Abstract
QuPath is a bioimage analysis software designed for digital pathology and whole slide image analysis. This protocol describes how to measure CD8 density in the substantia nigra and cerebral peduncle using haematoxylin and DAB-stained brain sections.
Materials
  • CD8 IHC-stained sections
  • NZConnect (Hamamatsu)
  • StarDist
  • QuPath
Annotation
Annotation
Manually annotate the substantia nigra and cerebral peduncle on NZConnect (Hamamatsu), a web-based whole-slide image (WSI) viewer.
Download the annotations using a Python script then import into QuPath [1] using a Groovy script.
QuPath Deconvolution and CD8 Density Measurement
QuPath Deconvolution and CD8 Density Measurement
In QuPath, set the colour deconvolution to facilitate the detection of haematoxylin and DAB staining on CD3 IHC-stained sections.
Segment all cell nuclei using StarDist [2] via the QuPath StarDist extension[3], follow with an object classifier to classify CD8-positive cells.
Calculate CD8-positive cell density was calculated by the number of CD8-positive cells divided by the area of the region of interest (CD8-positive cells per mm^2).
Note
References
[1] Bankhead, P., Loughrey, M.B., Fernández, J.A. et al. QuPath: Open source software for digital pathology image analysis. Sci Rep 7, 16878 (2017). https://doi.org/10.1038/s41598-017-17204-5

[2] Schmidt, U., Weigert, M., Broaddus, C., & Myers, G. (2018, September). Cell detection with star-convex polygons. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 265-273). Springer, Cham. https://arxiv.org/abs/1806.03535

[3] StarDist extension for QuPath
https://github.com/qupath/qupath-extension-stardist

Protocol references
[1] Bankhead, P., Loughrey, M.B., Fernández, J.A. et al. QuPath: Open source software for digital pathology image analysis. Sci Rep 7, 16878 (2017). https://doi.org/10.1038/s41598-017-17204-5

[2] Schmidt, U., Weigert, M., Broaddus, C., & Myers, G. (2018, September). Cell detection with star-convex polygons. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 265-273). Springer, Cham. https://arxiv.org/abs/1806.03535

[3] StarDist extension for QuPath
https://github.com/qupath/qupath-extension-stardist