Inferring cell communication using single-cell calcium spatiotemporal dynamics

There are a limited number of experimental tools for non-destructively discovering cell communication events in vitro and in vivo. Here, using tissue-specific genetically encoded calcium indicator (GECI) mice, we describe a protocol for preprocessing GECI fluorescence time-series measured by live cell imaging or intravital microscopy, detecting peaks of single-cell calcium fluorescence transients, and inferring putative cell communication events from peak synchrony. For complete details on the use and execution of this protocol, please refer to Taghdiri et al. (2021). [Display omitted] •Quantify single-cell calcium dynamics from cell-type-specific reporter cells and mice•Detect peaks of single-cell calcium transients and convert to binary impulse trains•Infer putative cell communication from the synchrony of single-cell impulse trains•Localize putative cell communication events in space and time Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. There are a limited number of experimental tools for non-destructively discovering cell communication events in vitro and in vivo. Here, using tissue-specific genetically encoded calcium indicator (GECI) mice, we describe a protocol for preprocessing GECI fluorescence time-series measured by live cell imaging or intravital microscopy, detecting peaks of single-cell calcium fluorescence transients, and inferring putative cell communication events from peak synchrony.