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An open-source pipeline for analysing changes in microglial morphology.

Devin Clarke1, Hans S Crombag1, Catherine N Hall1

  • 1School of Psychology and Sussex Neuroscience, The University of Sussex, Falmer, Brighton BN1 9QH, UK.

Open Biology
|August 10, 2021
PubMed
Summary

This study introduces an open-source pipeline for analyzing microglia morphology to assess brain inflammation. The new method, an

Keywords:
dimensionality reductionimage processingin vivomicrogliamorphologytwo-photon

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Area of Science:

  • Neuroscience
  • Immunology
  • Computational Biology

Background:

  • Microglial morphology changes serve as key indicators of neuroinflammation.
  • Quantifying these morphological changes is crucial for understanding brain inflammatory states.

Purpose of the Study:

  • To develop and validate an open-source pipeline for semi-automated microglia morphology analysis.
  • To generate a single, quantitative metric ('inflammation index') for assessing microglial inflammatory status.

Main Methods:

  • Image processing: Cleaning and registering microglia images using ImageJ.
  • Feature extraction: Quantifying 62 morphological parameters.
  • Dimensionality reduction: Developing an 'inflammation index' from control and inflammation training data.
  • Application: Assessing the impact of a high-fat diet on microglial morphology in Cx3CR1-GFP mice.

Main Results:

  • The pipeline successfully extracts 62 morphological parameters and generates an 'inflammation index'.
  • Short-term high-fat diet consumption in Cx3CR1-GFP mice showed no significant effect on microglial morphology.

Conclusions:

  • The developed open-source pipeline provides a robust and accessible method for microglia morphology analysis.
  • This tool facilitates the quantitative assessment of neuroinflammation across various experimental models.