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An automated approach to improve the quantification of pericytes and microglia in whole mouse brain sections


Courtney, J-M and Morris, GP and Cleary, EM and Howells, DW and Sutherland, BA, An automated approach to improve the quantification of pericytes and microglia in whole mouse brain sections, eNeuro, 8, (6) pp. 1-11. ISSN 2373-2822 (2021) [Refereed Article]

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Copyright Statement

Copyright 2021 by the Society for Neuroscience.

DOI: doi:10.1523/ENEURO.0177-21.2021


Whole slide scanning technology has enabled the generation of high-resolution images from complete tissue sections. However, commonly used analysis software is often unable to handle the large data files produced. Here, we present a method using the open-source software QuPath to detect, classify and quantify fluorescently-labeled cells (microglia and pericytes) in whole coronal brain tissue sections. Whole-brain sections from both male and female NG2DsRed x CX3CR1+/GFP mice were analyzed. Small regions of interest were selected and manual counts were compared with counts generated from an automated approach, across a range of detection parameters. The optimal parameters for detecting cells and classifying them as microglia or pericytes in each brain region were determined and applied to annotations corresponding to the entire somatosensory and motor cortices, hippocampus, thalamus, and hypothalamus in each section. 3.74% of all detected cells were classified as pericytes; however, this proportion was significantly higher in the thalamus (6.20%) than in other regions. In contrast, microglia (4.51% of total cells) were more abundant in the cortex (5.54%). No differences were detected between male and female mice. In conclusion, QuPath offers a user-friendly solution to whole-slide image analysis which could lead to important new discoveries in both health and disease.

Item Details

Item Type:Refereed Article
Keywords:pericyte, microglia, brain, mouse, QuPath, image processing, fluorescence microscopy
Research Division:Biomedical and Clinical Sciences
Research Group:Neurosciences
Research Field:Central nervous system
Objective Division:Expanding Knowledge
Objective Group:Expanding knowledge
Objective Field:Expanding knowledge in the biological sciences
UTAS Author:Courtney, J-M (Dr Jo-Maree Courtney)
UTAS Author:Morris, GP (Dr Gary Morris)
UTAS Author:Cleary, EM (Ms Elise Cleary)
UTAS Author:Howells, DW (Professor David Howells)
UTAS Author:Sutherland, BA (Associate Professor Brad Sutherland)
ID Code:147683
Year Published:2021
Funding Support:National Health and Medical Research Council (APP1137776)
Web of Science® Times Cited:5
Deposited By:Medicine
Deposited On:2021-11-11
Last Modified:2021-12-02
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