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MuSpAn was first conceived in 2016 by researchers at the University of Oxford, as a tool for quantitative analysis of cell locations from digital pathology images. Since 2021, the code has been developed with a focus on multiplex imaging data and, more recently, spatial transcriptomics, types of data which pose many problems for spatial analysis.

The guiding philosophy behind MuSpAn is that there is no "one right tool" for spatial data analysis - instead, different mathematical and statistical methods have different strengths at identifying different types of patterning in spatial data. MuSpAn is designed to bring complex mathematical methods into the world of biology, keeping the mathematical and coding knowledge prerequistites minimal while maximising the access of lab-based programmers to powerful spatial analysis tools.