Systems and methods for cell-type identification

A system for mapping a location of cell types within a tissue sample, the system comprising:

• one or more processors;
• and
• a non-transient memory in communication with the one or more processors and storing instructions, that when executed by the one or more processors are configured to cause the system to:
• receive image data of the tissue sample comprising a plurality of cell types distributed over a plurality of tissue regions of the tissue sample;
• generate a mapping estimate of cell types for each tissue region of the tissue sample based on the received image data;
• generate spatially resolved transcriptomic data for each tissue region of the tissue sample based on a plurality of cellular analyte molecules extracted from the tissue sample, wherein each of the plurality of cellular analyte molecules are associated with a respective cell type of the plurality of cell types by using a spatial transcriptomics platform to process the extracted plurality of cellular analyte molecules;
• determine cell-type reference data comprising gene expression by cell type for each cell type of the tissue sample;
• and
• output a feature map of the tissue sample comprising a final inferred cell type compositional map for each tissue region of the tissue sample based on the spatially resolved transcriptomic data, the determined cell-type reference data, and the mapping estimate of cell types.