An Open-source Pipeline for Analysing Changes in Microglial Morphology

Overview

Journal Open Biol

Specialties Biology
Cell Biology
Molecular Biology

Date 2021 Aug 10

PMID 34375551

Citations 10

Authors

Devin Clarke

Hans S Crombag

Catherine N Hall

Affiliations

Soon will be listed here.

Abstract

Changes 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.

Citing Articles

Streamlined Quantification of Microglial Morphology in Mouse Brains Using 3D Immunofluorescence Analysis.

de Donato M, Kouchaeknejad A, de Donato A, Van Der Walt G, Puighermanal E Bio Protoc. 2025; 15(4):e5218.

PMID: 40034468 PMC: 11873448. DOI: 10.21769/BioProtoc.5218.

Development of a High-Throughput Pipeline to Characterize Microglia Morphological States at a Single-Cell Resolution.

Kim J, Pavlidis P, Ciernia A eNeuro. 2024; 11(7).

PMID: 39029952 PMC: 11289588. DOI: 10.1523/ENEURO.0014-24.2024.

Microglial reactivity in brainstem chemosensory nuclei in response to hypercapnia.

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PMID: 38476146 PMC: 10927973. DOI: 10.3389/fphys.2024.1332355.

Monoclonal Antibody Therapy in Alzheimer's Disease.

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Microglial morphometric analysis: so many options, so little consistency.

Reddaway J, Richardson P, Bevan R, Stoneman J, Palombo M Front Neuroinform. 2023; 17:1211188.

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