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Space Ranger Segment Specifications

Process Details

  • Name: Space Ranger Segment
  • Process UUID: 47a61cc4bcb148e7abfef13db65fd184
  • Process Group: Spatial

Overview

This process runs 10x Genomics' Space Ranger segment pipeline on microscope images to perform cell segmentation for spatial gene expression analysis. The process identifies and segments individual cell nuclei from tissue microscopy images, creating instance masks and boundary definitions that can be used for downstream spatial analysis.

This process is implemented in Bash, utilizing the Space Ranger software suite for spatial transcriptomics data processing.

Key Functionality

  • Image Preprocessing: Handles compressed and uncompressed microscope images, automatically decompressing when necessary
  • Cell Segmentation: Identifies and segments individual cell nuclei using Space Ranger's segmentation algorithms
  • Instance Mask Generation: Creates pixel-level instance masks for each segmented nucleus
  • Boundary Detection: Generates geometric boundary definitions in GeoJSON format for visualization and analysis

Input/Output Specification

Inputs

Required Inputs

  • Samplesheet
    • Description: Configuration file containing sample metadata and file paths for the segmentation analysis
    • Format: Samplesheet format

Outputs

  • Output TGZ

    • Description: Compressed archive containing all Space Ranger segment output files
    • Format: TGZ (compressed tar archive)

  • TIFF File

    • Description: Nucleus instance mask as a TIFF image showing segmented cell boundaries
    • Format: TIFF

  • Output HTML

    • Description: Web summary report with segmentation quality metrics and visualizations
    • Format: HTML

  • JSON

    • Description: Nucleus segmentations in GeoJSON format containing geometric boundary definitions
    • Format: JSON

Parameters & Settings

No user-configurable parameters are available for this process. The segmentation uses default Space Ranger parameters with a maximum nucleus diameter of 256 pixels.

References & Resources

  • Tool Documentation: 10x Genomics Space Ranger Documentation
  • Related Papers: Ståhl, P.L., Salmén, F., Vickovic, S. et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353, 78-82 (2016). DOI: 10.1126/science.aaf2403