Fig. 1: Computational immune synapse analysis.

a Individual synapse strength \(\sigma\) is the logarithm of the mean membrane signal intensity of CD3 at the T-cell-_APC contact interface relative to the intensity outside the contact interface. b Image level synapse strength \(\bar{{\rm{\sigma }}}\) is the average over all neighboring cell-cell pairs in the image. Statistically, \(\bar{{\rm{\sigma }}}\) < 0 indicates a lack of interaction; \(\bar{{\rm{\sigma }}}\) > 0 indicates an active interaction. Showing an example diagram of \(\bar{{\rm{\sigma }}}\) > 0. c The general niche of CISA in an image-based analysis workflow. CISA takes three required inputs, namely single channel images, a raster cell segmentation mask image, and the cell classification. CISA outputs a table of \({\rm{\sigma }}\) at each T-neighbor interface, which can be then aggregated for sample level \(\bar{{\rm{\sigma }}}\) for statistical characterization.