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bioRxiv · 10.64898/2026.05.12.724373

Differential Analysis of Gene Spatial Organisation with Minkowski Functionals and Tensors

Baratta, P.·Villoutreix, P.·Baudot, A.
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Abstract

Spatial transcriptomics measures gene expression together with transcript coordinates in tissues. To date, comparing spatial gene expression patterns within and across samples remains challenging. We present here minkiPy, a geometric framework that computes, for each gene, a compact profile of morphological and topological descriptors based on Minkowski functionals and tensors. These profiles are defined in a shared feature space, enabling direct comparison of spatial organisation across genes, samples, and conditions, and the ranking of genes by the magnitude of their spatial reorganisation. We applied minkiPy to a MERFISH dataset of control and facioscapulohumeral muscular dystrophy myoblast cultures and to a Visium HD dataset of colorectal cancer and normal adjacent tissues, illustrating its utility across tissue types and spatial transcriptomics platforms. minkiPy is an open-source Python library available at https://github.com/BAUDOTlab/minkiPy.

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Baratta, P., Villoutreix, P., Baudot, A.. 2026-05-14. Differential Analysis of Gene Spatial Organisation with Minkowski Functionals and Tensors. https://doi.org/10.64898/2026.05.12.724373

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