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Spatial H5ad To Seurat Specifications

Process Details

  • Name: spatial_h5ad_to_seurat
  • Process UUID: c6634w3z38ivun71gzd8v7zbeyjds7
  • Process Group: Spatial

Overview

This process converts spatial transcriptomics data from the scanpy h5ad format to Seurat RDS format, specifically designed for Visium spatial data. The conversion enables seamless transition between Python-based scanpy workflows and R-based Seurat analysis pipelines while preserving spatial information and metadata.

This process is implemented in Bash, which invokes an R script using the schard package for format conversion.

Key Functionality

  • Format Conversion: Transforms h5ad files (scanpy format) to RDS files (Seurat format)
  • Spatial Data Preservation: Maintains spatial coordinates and tissue position information during conversion
  • Metadata Retention: Preserves cell and gene metadata, annotations, and analysis results
  • Seurat Object Creation: Generates properly formatted Seurat objects ready for downstream spatial analysis

Input/Output Specification

Inputs

Required Inputs

  • H5AD File
    • Description: Spatial transcriptomics data in h5ad format from scanpy analysis
    • Format: h5ad

Outputs

  • RDS File
    • Description: Seurat object containing the converted spatial transcriptomics data with preserved spatial coordinates and metadata
    • Format: RDS

Parameters & Settings

This process does not have user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on schard package usage
  • Related Papers: Stuart, T., Butler, A., Hoffman, P. et al. Comprehensive Integration of Single-Cell Data. Cell 177, 1888-1902.e21 (2019). https://doi.org/10.1016/j.cell.2019.05.031