Dec 07, 2023

Public workspaceAT8 Tau Pathology Image Analysis V.1

DOI
https://dx.doi.org/10.17504/protocols.io.n2bvj386wlk5/v1
AT8 Tau Pathology Image Analysis
  • Hemanth Ramesh Nelvagal1,2,
  • Toby Curless1,2,
  • Zane Jaunmuktane1,3,2
  • 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
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DOI: https://dx.doi.org/10.17504/protocols.io.n2bvj386wlk5/v1
Protocol Citation: Hemanth Ramesh Nelvagal, Toby Curless, Zane Jaunmuktane 2023. AT8 Tau Pathology Image Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.n2bvj386wlk5/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 03, 2023
Last Modified: May 31, 2024
Protocol Integer ID: 85939
Keywords: ASAPCRN, AT8 Tau, Pathology, Human Brain, Parkinson's disease, QuPath, NZConnect, Image Analysis, at8 tau pathology image analysis qupath, at8 tau pathology in human brain tissue, at8 tau pathology, bioimage analysis software, digital pathology, image analysis, ffpe sections with ihc, whole slide image analysis, human brain tissue, ihc, ffpe section
Funders Acknowledgements:
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 analyse AT8 tau pathology in human brain tissue (FFPE sections with IHC).
Materials
Troubleshooting
Annotation
Manually annotate regions of interest on NZConnect (Hamamatsu), a web-based whole-slide image (WSI) viewer:https://www.hamamatsu.com/us/en/product/life-science-and-medical-systems/digital-slide-scanner/U16179-01.html.
Download annotations using a Python script.


QuPath De-Convolution and Measurements
Import into QuPath using a Groovy script. Refer to: 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
In QuPath, apply colour deconvolution to distinguish DAB from the haematoxylin counterstain.
Measure the area of positive DAB staining for tau pathology using a fixed threshold value of 0.2 on the DAB deconvolved channel.
Calculate the percentage of positive DAB staining within the ROI by calculating  the area of positive DAB staining divided by the area of the ROI and multiplied by 100.



Protocol references
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