Mapping Microglial Parameters Software (MMPS): An Open-Source, User-Friendly Tool for Quantitative Microglia Morphology Analysis.

Microglia are myeloid-derived immune cells of the central nervous system that mediate tissue degradation and remodeling following neurological injury and have emerged as promising therapeutic targets in several neurodegenerative diseases. Quantitative analysis of microglial morphology can reveal subtle differences among microglial subpopulations while preserving important in situ information. However, many currently available microglial morphology analysis platforms are either not publicly accessible or require specialized computational expertise, thereby limiting their widespread adoption. To address these limitations, an open-source microglial morphology analysis platform, termed Mapping Microglial Parameters Software (MMPS), using Python 3.11 was developed. MMPS is compatible with immunofluorescence-based workflows and requires no coding expertise for installation or operation. The software semi-automates single-cell microglial morphology analysis through an accessible graphical user interface and incorporates customizable image-processing and mask-generation workflows. The study involves validating MMPS using a rodent lipopolysaccharide (LPS)-induced neuroinflammation model. Quantitative animal-level analysis demonstrated that microglia from LPS-treated animals exhibited significantly increased soma area (p < 0.01) and reduced cell perimeter (p < 0.05) compared with vehicle-treated controls, consistent with morphological features associated with microglial activation and neuroinflammation. Overall, MMPS provides a standardized, reproducible platform for quantitative analysis of microglial morphology across laboratories.