The software supports anatomical images from public repositories (e.g. EBI anatomogram) or those created by users. In general any type of image can be used as long as it can be provided in SVG (Scalable Vector Graphics) format and the corresponding spatial features, such as organs, tissues, cellular compartments, are annotated with unique identifiers.

The spatialHeatmap software provides novel functionalities to integrate tissue and single-cell data by visualizing them in composite plots that combine SHMs with embedding plots of high-dimensional data. Identical colors indicate matching components between SHM and embedding plots.

To appeal to both non-expert and computational users, spatialHeatmap provides a graphical and command-line interface, respectively. It is distributed as a free, open-source Bioconductor package (https://bioconductor.org/packages/spatialHeatmap) that users can install on personal computers, shared servers, or cloud systems.

SHMs are a powerful visualization tool for focused analyses routines comparing assay profiles among smaller numbers of biomolecules across cell types and conditions. This is the case because each biomolecule requires its own SHM plot.

The primary utility of spatial enrichment is the automated detection of groups of biomolecules with enriched or depleted abundance in the profiled spatial features, and subsequently visualize these patterns in SHMs.