Points2Regions: Fast Interactive Clustering of in Situ Transcriptomics Data

Investigation of the spatial cellular architecture in tissue is crucial for furthering our understanding of biological processes and diseases. The location of different cell types can be revealed by multiplexed in situ RNA detection. Most of the analysis algorithms for in situ transcriptomics (IST) rely on cell segmentation or prior biological knowledge from complementary single-cell sequencing experiments. Here, we present Points2Regions, a fast and simple tool for interactive clustering and exploration of IST data. This tool comes as a plugin in TissUUmaps 3, making it accessible to an audience without programming experience. Points2Regions defines regions with similar composition of mRNA-markers. The regions are directly displayed on top of large-scale image data in TissUUmaps 3, making visual exploration easy. The tool is computationally efficient and can run without the need of any specialized hardware.