Quantification of Microglia Morphology from whole Piglet Brain Brightfield Images
Collaboration
S. Pankratova, Comparative Pediatrics, Faculty of Health and Medical Sciences, Copenhagen University
Research Background
Inflammation in the gut can influence brain health, with notable effects on the morphology of microglia cells. Microglia cells in healthy tissue typically exhibit fine, branching processes, while inflamed tissue shows thicker, darker cell bodies with fewer branches. This project quantifies microglia morphology in pig hippocampus tissue stained with H-DAB, using brightfield microscopy to study the effects of gut inflammation on the brain.
Method
Development of an automated pipeline combining QuPath and ImageJ to analyze microglia morphology in histological images. The pipeline comprises:
Cell Body Detection: Identification of DAB-positive microglia soma within annotated regions using QuPath
Preprocessing, Segmentation and Skeletonization: Cropped regions around detected cells are exported to ImageJ for pre-filtering, thresholding and skeletonization of the segmented cells
Skeleton Analysis & Data Output: Morphological metrics, including the number of branches, junctions, endpoints, and average process length, are quantified from the skeletonized microglia. Results are saved as Excel files for statistical analysis, and the skeletons are returned to QuPath as overlays for visual verification.