SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data

Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors ("Catching up with Multiplexed Tissue Imaging," 2022). A critical aspect of such "tissue profiling" is quantifying the spatial relationships among cells at different scales from the interaction of neighboring cells to recurrent communities of cells of multiple types. This often involves statistical analysis of 10⁷ or more cells in which up to 100 biomolecules (commonly proteins) have been measured. While software tools currently cater to the analysis of spatial transcriptomics data (Liu et al., 2022), there remains a need for toolkits explicitly tailored to the complexities of multiplexed imaging data including the need to seamlessly integrate image visualization with data analysis and exploration. We introduce SCIMAP, a Python package specifically crafted to address these challenges. With SCIMAP, users can efficiently preprocess, analyze, and visualize large datasets, facilitating the exploration of spatial relationships and their statistical significance. SCIMAP's modular design enables the integration of new algorithms, enhancing its capabilities for spatial analysis.