Neuroscience JoVE (Open Access) Citable · DOI

Quantifying Microglia Morphology from Photomicrographs of Immunohistochemistry Prepared Tissue Using ImageJ

Name: Quantifying Microglia Morphology from Photomicrographs of Immunohistochemistry Prepared Tissue Using ImageJ
Uploaded: 2026-08-05
Duration: 8 min 44 s
Description: Microglia are brain phagocytes that participate in brain homeostasis and continuously survey their environment for dysfunction, injury, and disease. As ...

DOI: 10.3791/57648-v

What you'll learn

✓ Apply skeleton analysis to quantify microglia cell ramification and branching complexity
✓ Use fractal analysis to measure microglia morphological complexity from immunohistochemistry images
✓ Convert qualitative microglia morphology into continuous quantitative data using ImageJ

Protocol

Biopharma Insights Microglia are brain immune cells that survey and react to altered brain physiology through morphologic changes which may be evaluated quantitatively. This protocol outlines an ImageJ based analysis protocol to represent microglia morphology as continuous data according to metrics such as cell ramification, complexity, and shape.

Difficulty

intermediate

Total time

~1-2 hrs per tissue section (depending on number of cells analyzed)

Model organism

Mouse

Steps

Perform skeleton analysis on microglia

Convert immunohistochemistry images of microglia to binary format and apply ImageJ skeletonization to extract cell ramification patterns, measuring branch length and complexity metrics.

▶ 00:51

Apply fractal analysis to microglia morphology

Use fractal dimension analysis in ImageJ to quantify the self-similar complexity of microglia cell structure, generating a continuous metric independent of cell size.

▶ 05:10

Compare quantitative results with and without protocol

Validate the analysis by comparing morphological data obtained using the standardized protocol against unprocessed or alternative analysis approaches.

▶ 07:19

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