Semi-Automated CellProfiler Pipelines for Robust Quantification of Microglial Density, Distribution and Morphology

The field of microglial research has evolved throughout the years. Microglia, the immune cells of the central nervous system, are recognized as highly heterogeneous and dynamic cells, known for modifying their structure and function based on the local context. Investigating microglial density, spatial distribution, and morphological states is important for uncovering their distinct functional states in health and pathology. However, quantifying these features accurately is often a methodological challenge. Fully automated computational approaches often fail to capture subtle biological nuances and complex structural variations. Also, the high diversity of image sets makes it difficult to maintain consistent reliability. In contrast, entirely manual quantification is labor-intensive and prone to observer bias. To bridge this gap, we propose a semi-automated framework using the open-source software CellProfiler. Our workflow is divided into two distinct pipelines designed to combine automation of batch analysis with targeted user oversight, allowing for manual intervention when necessary to ensure maximum accuracy. Both pipelines are capable of recognizing microglial soma and tracing their processes. In the density workflow, it automatically calculates cell density and provides spatial distribution measurements, such as closest-neighbor distance and spacing index. For morphological profiling, it yields extensive structural data, including area, perimeter, convex area, form factor, and various shape descriptors. Furthermore, we demonstrate how researchers can optimize the pipeline settings to accommodate varied image datasets and experimental conditions. We hope this open-source framework can standardize microglial density, distribution, and morphological analysis and reduce systematic bias, providing researchers with a robust tool to better characterize their heterogeneity.