Spatialsnake Pipeline for Spatial Transcriptomics
What is Spatialsnake?
Spatialsnake is a command-line workflow for reproducible spatial transcriptomics analysis. It is designed to help users with different computational backgrounds process spatial datasets through concise commands and transparent YAML configuration files.
What can Spatialsnake do?
Spatialsnake supports data ingestion, preprocessing, clustering, cell-type annotation, subcluster refinement, and downstream analysis for single-sample and integrated spatial transcriptomics projects.
What is distinctive about Spatialsnake?
Spatialsnake is built on the scverse ecosystem and uses SpatialData Zarr objects to organize platform-specific expression, image, shape, label, and coordinate information in a unified data structure. It also provides reusable utilities for sample or region splitting, annotation overlay, sample merging, and controlled conversion to AnnData H5AD or Seurat RDS.
Why use Spatialsnake?
Spatial transcriptomics projects often require repeated data restructuring as analytical questions change. Spatialsnake reduces ad hoc file handling while preserving identifiers, metadata, and spatial relationships across analysis steps, making routine workflows easier to reproduce and transfer between projects.
Note
This tutorial assumes basic familiarity with the Linux command line. Replace example paths, parameters, and sample names with values appropriate for your own project. If spatial transcriptomics workflows are new to you, read the module overview and input requirements before running each command.
Tutorial Contents
Getting Started
Data Ingestion
Main Analysis