MuSpAn: A Toolbox for Multiscale Spatial Analysis

The generation of spatial data in biology has been transformed by multiplex imaging and spatial-omics technologies, such as single cell spatial transcriptomics. These approaches permit detailed mapping of phenotypic information about individual cells and their spatial locations within tissue sections. Quantitative methods for maximising the information that can be retrieved from these images have not kept pace with technological developments, and no standard methodology has emerged for spatial data analysis. Proposed pipelines are often tailored to individual studies, leading to a fragmented landscape of available methods, and no clear guidance about which statistical tools are best suited to a particular question. In response to these challenges, we present MuSpAn, a Multiscale Spatial Analysis package designed to provide straightforward access to both well-established and cutting-edge mathematical analysis tools. MuSpAn provides easy to use, flexible, and interactive access to quantitative methods from fields including spatial statistics, topological data analysis, network theory, geometry, probability and ecology. Users can construct custom pipelines from across these fields to address specific biological problems, or conduct unbiased exploration of their data for discovery spatial biology. In summary, MuSpAn is an extensive platform which enables multiscale analysis of spatial data, ranging from the subcellular to the tissue-scale.