Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.05.284539v1?rss=1 Authors: Bao, F., Deng, Y., Wan, S., Wang, B., Dai, Q., Altschuler, S., Wu, L. Abstract: Advances in spatial transcriptomics technologies enable optical profiling of morphological and transcriptional modalities from the same cells within tissues. Here, we present multi-modal structured embedding (MUSE), an approach to deeply characterize tissue heterogeneity through analysis of combined image and transcriptional single-cell measurements. We demonstrate that MUSE can discover cellular subpopulations missed by either modality as well as compensate for modality-specific noise. MUSE identified biologically meaningful cellular subpopulations and stereotyped spatial patterning within heterogeneous mouse cortex brain tissues, profiled by seqFISH+ or STARmap technologies. MUSE provides a framework for combining multi-modal single-cell data to reveal deeper insights into the states, functions and organization of cells in complex biological tissues. Copy rights belong to original authors. Visit the link for more info