Spatialsnake Pipeline for Spatial Transcriptomics
Spatialsnake is an automated pipeline for spatial transcriptomics analysis.
Implemented in Python on top of the scverse ecosystem, Spatialsnake uses SpatialData to convert datasets from multiple spatial transcriptomics platforms into a unified zarr-based object format.
This design provides a consistent computational framework spanning data ingestion, preprocessing, clustering, annotation, and downstream analysis, while preserving compatibility with platform-specific inputs.
By combining a command-line interface with workflow-based parameter control, Spatialsnake emphasizes reproducibility, operational clarity, and ease of adoption, enabling end-to-end spatial transcriptomics analysis without extensive custom scripting or repeated environment setup.
Note
This tutorial assumes basic familiarity with the Linux command line and the ability to run standard commands after replacing paths, parameters, and sample names as needed. If you are not yet familiar with the standard workflow of spatial transcriptomics analysis, we recommend reading the overview and explanatory notes in each module carefully. Spatialsnake is designed to lower the technical barrier to bioinformatics analysis through a user-friendly command-line framework, so that scientific investigation is not limited by computational background.
Tutorial Contents
Getting Started
Data Ingestion
Main Analysis