Figure 1. The image processing strategy for segmenting cell shape of individual microglia.

Cell positions (CP, blue cross) within a maximum intensity projection were identified by a local maxima-finding algorithm. Within a 120×120 µm local region (LR, white square) centered per CP, cell masks (CM) are segmented through an iterative local threshold algorithm. For each CM, a cell soma mask (CSM) is defined as an object with pixel values greater than the last iterative threshold+50% and contiguous area greater than 16.7 µm². A CM (red outline) and CSM (white outline) are considered accurate representations of a cell (bottom figure) if the CM is not touching the edge of the LR boundary and has a single CSM. Scale bar equals 50 µm.