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Spaceranger to AnnData Specifications

Process Details

  • Name: Spaceranger to AnnData
  • Process UUID: ef40857a06db4dc48ac73987735cdc6e
  • Process Group: Spatial

Overview

This process converts Space Ranger output data into AnnData format for downstream spatial transcriptomics analysis. The process extracts Space Ranger results, integrates segmentation masks, and creates a standardized AnnData object with configurable spatial binning parameters.

This process is implemented in Bash, which invokes a Python script for spatial data processing and AnnData construction.

Key Functionality

  • Space Ranger Data Extraction: Extracts and processes compressed Space Ranger output files
  • Spatial Binning Configuration: Applies user-specified bin sizes for spatial data organization
  • Segmentation Integration: Incorporates segmentation masks into the spatial analysis workflow
  • AnnData Generation: Creates standardized AnnData objects compatible with spatial analysis pipelines

Input/Output Specification

Inputs

Required Inputs

  • Space Ranger Output

    • Description: Compressed Space Ranger output directory containing spatial transcriptomics data
    • Format: tar.gz

  • TIFF Image File

    • Description: High-resolution tissue image file for spatial visualization
    • Format: TIFF

Outputs

  • AnnData Object
    • Description: Processed spatial transcriptomics data in AnnData format with integrated spatial coordinates and segmentation information
    • Format: H5AD

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Target Bin Size

    • Description: Target bin size to use for constructing AnnData
    • Available options: 2µm, 8µm (default), 16µm

  • Mask File Format

    • Description: Which segmentation file to use (Different from Nucleus Mask)
    • Available options: geojson (default), tiff

References & Resources

  • Tool Documentation: Contact the team for details on visium_scanpy_pipeline.py