Cargando…

An open-source pipeline for analysing changes in microglial morphology

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 compa...

Descripción completa

Detalles Bibliográficos
Autores principales: Clarke, Devin, Crombag, Hans S., Hall, Catherine N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8354754/
https://www.ncbi.nlm.nih.gov/pubmed/34375551
http://dx.doi.org/10.1098/rsob.210045
_version_ 1783736645335384064
author Clarke, Devin
Crombag, Hans S.
Hall, Catherine N.
author_facet Clarke, Devin
Crombag, Hans S.
Hall, Catherine N.
author_sort Clarke, Devin
collection PubMed
description 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.
format Online
Article
Text
id pubmed-8354754
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher The Royal Society
record_format MEDLINE/PubMed
spelling pubmed-83547542021-12-14 An open-source pipeline for analysing changes in microglial morphology Clarke, Devin Crombag, Hans S. Hall, Catherine N. Open Biol Methods and Techniques 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. The Royal Society 2021-08-11 /pmc/articles/PMC8354754/ /pubmed/34375551 http://dx.doi.org/10.1098/rsob.210045 Text en © 2021 The Authors. https://creativecommons.org/licenses/by/4.0/Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, provided the original author and source are credited.
spellingShingle Methods and Techniques
Clarke, Devin
Crombag, Hans S.
Hall, Catherine N.
An open-source pipeline for analysing changes in microglial morphology
title An open-source pipeline for analysing changes in microglial morphology
title_full An open-source pipeline for analysing changes in microglial morphology
title_fullStr An open-source pipeline for analysing changes in microglial morphology
title_full_unstemmed An open-source pipeline for analysing changes in microglial morphology
title_short An open-source pipeline for analysing changes in microglial morphology
title_sort open-source pipeline for analysing changes in microglial morphology
topic Methods and Techniques
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8354754/
https://www.ncbi.nlm.nih.gov/pubmed/34375551
http://dx.doi.org/10.1098/rsob.210045
work_keys_str_mv AT clarkedevin anopensourcepipelineforanalysingchangesinmicroglialmorphology
AT crombaghanss anopensourcepipelineforanalysingchangesinmicroglialmorphology
AT hallcatherinen anopensourcepipelineforanalysingchangesinmicroglialmorphology
AT clarkedevin opensourcepipelineforanalysingchangesinmicroglialmorphology
AT crombaghanss opensourcepipelineforanalysingchangesinmicroglialmorphology
AT hallcatherinen opensourcepipelineforanalysingchangesinmicroglialmorphology