SpatialOne: end-to-end analysis of visium data at scale

Spatial transcriptomics allow to quantify mRNA expression within the spatial context. Nonetheless, in-depth analysis of spatial transcriptomics data remains challenging and difficult to scale due to the number of methods and libraries required for that purpose.

Here we present SpatialOne, an end-to-end pipeline designed to simplify the analysis of 10x Visium data by combining multiple state-of-the-art computational methods to segment, deconvolve, and quantify spatial information; this approach streamlines the analysis of reproducible spatial-data at scale.

SpatialOne source code and execution examples are available at https://github.com/Sanofi-Public/spatialone-pipeline, experimental data is available at https://zenodo.org/records/12605154. SpatialOne is distributed as a docker container image.