Spatialsnake: a flexible workflow for spatial transcriptomics analysis across platforms

Spatialsnake is a unified SpatialData–Snakemake workflow that supports Visium, Visium HD, Stereo-seq, Xenium, and MERFISH, enabling flexible re-clustering and label mapping across datasets.

• Why it matters: Spatial transcriptomics outputs vary by platform and spatial resolution, and extending analyses to selected populations or tissue regions often requires extra scripting and repeated data preparation.
• What they did: The workflow provides a common command-line interface for single- and multi-sample analysis with adjustable parameters and saved intermediates, plus modules for composition, spatial domains, communication, and regulons.
• The result: In mouse-brain Visium and colorectal cancer Visium HD, joint analysis of three colorectal cancer sections retained 1,527,987 bins and enabled further analysis of 223,632 epithelial bins linked to their locations.