Protocol for total internal reflection fluorescence microscopy image preprocessing and radial analysis of LFA-1 in T cell immune synapses

Here, we present a protocol for total internal reflection fluorescence (TIRF) microscopy image preprocessing and radial analysis of lymphocyte function-associated antigen-1 (LFA-1) in T cell immune synapses. We describe steps for combining customizable Fiji/ImageJ macros for image background subtraction and segmentation with flexible R-based scripts for peripheral supramolecular activation cluster (pSMAC) center identification, center-based cropping, and radial analysis of synaptic LFA-1 in T cells. This workflow supports established analyses, including radial averaging/spinning and fluorescence intensity measurements across the synapse.