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Space Ranger Pipeline Specification

Pipeline Details

  • Name: Space Ranger Pipeline
  • Pipeline UUID: be6acb4979ea4a59b046539484691227
  • Version: 1.0.12
  • View Pipeline:

Overview

Space Ranger Pipeline is designed to run the Space Ranger software (v3.0 and later) to analyze Visium HD Spatial Gene Expression datasets. It supports datasets generated from formalin-fixed paraffin-embedded (FFPE) human or mouse samples processed using the Visium CytAssist instrument. The pipeline seamlessly handles high-resolution spatial transcriptomics data, unlocking insights into tissue-specific gene expression patterns and generates Batch Corrected (Harmony) Seurat objects for downstream analysis.

Key Use cases:

  • Visium HD Spatial Transcriptomics Analysis: Process high-resolution spatial gene expression data from FFPE samples using the CytAssist instrument.
  • Tissue Architecture Analysis: Map gene expression patterns to specific tissue structures and spatial contexts.
  • Multi-sample Integration: Batch correct and integrate multiple spatial samples using Harmony algorithm for comparative studies.

Features

  • High-Resolution Spatial Analysis: Supports Visium HD datasets with multiple bin sizes (2μm and 8μm) for flexible spatial resolution analysis.
  • Comprehensive Output Generation: Produces gene expression matrices, interactive .cloupe files for Loupe Browser visualization, and spatial imaging data.
  • Seurat Integration: Automatic conversion to Seurat objects with quality control, normalization, and dimensionality reduction.
  • Batch Correction: Implements Harmony-based batch correction for multi-sample integration studies.
  • Multi-format Export: Generates both RDS (Seurat) and h5ad (AnnData) formats for compatibility with R and Python ecosystems.
  • Quality Control Pipeline: Automated filtering based on gene detection rates, UMI counts, and mitochondrial/ribosomal gene content.

Input/Output Specification

Inputs

The pipeline accepts standard Space Ranger inputs through its processes but does not define specific pipeline-level input parameters in the current configuration.

Outputs

Reported Outputs

  • Integrated Seurat Object:
  • Description: Batch-corrected and integrated Seurat object containing all samples with dimensional reduction and clustering
  • Format: .rds
  • Visualization App: R/Seurat, DE Browser

  • Location: Integration results folder

  • Individual Sample Seurat Objects:

  • Description: Quality-controlled Seurat objects for each sample with spatial coordinates and metadata
  • Format: .rds
  • Visualization App: R/Seurat

  • Location: Sample-specific analysis folders

  • h5ad Files:

  • Description: AnnData format files converted from Seurat objects for Python-based analysis
  • Format: .h5ad
  • Visualization App: Scanpy, CellxGene, Python notebooks
  • Location: Sample output directories

Supporting Outputs

  • Cloupe Files:
  • Description: Interactive visualization files for 10x Genomics Loupe Browser
  • Format: .cloupe
  • Visualization App: Loupe Browser

  • Location: Space Ranger output directories

  • Feature Matrices:

  • Description: Filtered and raw gene expression count matrices in HDF5 format
  • Format: .h5

  • Location: Space Ranger binned outputs

  • Web Summary Reports:

  • Description: HTML reports containing quality metrics and analysis summaries
  • Format: .html

  • Location: Sample analysis directories

  • Spatial Data:

  • Description: Spatial coordinates and tissue images for spatial visualization
  • Format: Various (JSON, PNG, TIFF)
  • Location: Spatial output directories

Associated Processes

References & Additional Documentation