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An open-source pipeline for analysing changes in microglial morphology
Version 2 2023-06-12, 08:07
Version 1 2023-06-10, 01:21
journal contribution
posted on 2023-06-12, 08:07 authored by Devin Clarke, Hans CrombagHans Crombag, Catherine HallCatherine HallChanges in microglial morphology are powerful indicators of the inflammatory state of the brain. Here, we provide an open-source microglia morphology analysis pipeline that first cleans and registers images of microglia, before extracting 62 parameters describing microglial morphology. It then compares control and 'inflammation' training data and uses dimensionality reduction to generate a single metric of morphological change (an 'inflammation index'). This index can then be calculated for test data to assess inflammation, as we demonstrate by investigating the effect of short-term high-fat diet consumption in heterozygous Cx3CR1-GFP mice, finding no significant effects of diet. Our pipeline represents the first open-source microglia morphology pipeline combining semi-automated image processing and dimensionality reduction. It uses free software (ImageJ and R) and can be applied to a wide variety of experimental paradigms. We anticipate it will enable others to more easily take advantage of the powerful insights microglial morphology analysis provides.
History
Publication status
- Published
File Version
- Published version
Journal
Open BiologyISSN
2046-2441Publisher
The Royal SocietyExternal DOI
Issue
8Volume
11Page range
210045 1-15Event location
EnglandDepartment affiliated with
- Psychology Publications
Full text available
- Yes
Peer reviewed?
- Yes
Legacy Posted Date
2021-10-08First Open Access (FOA) Date
2021-10-08First Compliant Deposit (FCD) Date
2021-10-07Usage metrics
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