SpatialSPM: Statistical parametric mapping for the comparison of gene expression pattern images in multiple spatial transcriptomic datasets

Spatial transcriptomic (ST) techniques help us understand the gene expression levels in specific parts of tissues and organs, providing insights into their biological functions. Even though ST dataset provides information on the gene expression and its location for each sample, it is challenging to compare spatial gene expression patterns across tissue samples with different shapes and coordinates. Here, we propose a method that reconstructs ST data into multi-dimensional image matrices to ensure comparability across different samples through spatial registration process. We demonstrated the applicability of this method by using two mouse brain ST datasets to investigate and directly compare gene expression in a specific anatomical region of interest, pixel by pixel, across various biological statuses. It can produce statistical parametric maps to find specific regions with differentially expressed genes across tissue samples. Our approach provides an efficient way to analyze ST datasets and may offer detailed insights into various biological conditions.