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Xenium Spatial Analysis Pipeline Specification

Pipeline Details

  • Name: Xenium Spatial Analysis Pipeline
  • Pipeline UUID: 73d46e9d615d46e893b7a1a2421e8ae1
  • Version: 1.0.3
  • View Pipeline:

Overview

Xenium Spatial Analysis Pipeline is designed for comprehensive spatial transcriptomics analysis of 10x Genomics Xenium data. It automates data preprocessing, quality control, and downstream spatial analysis to provide high-resolution, subcellular RNA imaging insights across tissue sections with quantitative spatial gene expression mapping.

Key Use cases:

  • Spatial Transcriptomics Analysis: Processing Xenium output data for high-resolution spatial gene expression mapping at subcellular resolution.
  • Tissue Microenvironment Mapping: Analyzing cellular organization and tissue architecture through spatial gene expression patterns.
  • Quality Control and Visualization: Generating comprehensive QC reports and interactive visualizations for spatial genomics data interpretation.

Features

  • Xenium Data Processing: Native support for 10x Genomics Xenium output formats including .zip archives with comprehensive file structure handling.
  • Flexible Segmentation Options: Supports cell, nucleus, or no boundary segmentation for spatial visualization and analysis.
  • Automated Quality Control: Implements configurable threshold-based filtering with quantile-based cutoffs for transcript molecules and genes per cell.
  • Comprehensive Reporting: Generates detailed HTML reports with QC metrics, clustering analysis, and spatial visualizations using R/Seurat integration.
  • Scalable Processing: Containerized workflow using specialized Docker images (ubuntu-seurat:5.3.0) for reproducible spatial transcriptomics analysis.
  • Multi-format Output: Produces both RDS objects for downstream analysis and interactive HTML reports for immediate visualization.

Input/Output Specification

Inputs

Required

Xenium Output Directory

  • Description: Xenium output data containing spatial transcriptomics results, typically provided as a .zip archive or directory structure from 10x Genomics Xenium instrument.
  • Format: .zip archive or directory containing standard Xenium output files (cell_feature_matrix, transcripts, morphology images, etc.)
  • Example File Path: /path/to/xenium_output.zip

Sample Sheet

  • Description: Sample metadata file containing sample information and processing parameters for the spatial analysis workflow.
  • Format: Tab-separated values (.tsv)
  • Example File Path: /path/to/samplesheet.tsv

Optional Inputs

Cell Statistics File

  • Description: Additional cell-level statistics file for enhanced quality control and filtering.
  • Format: Various formats supported
  • Example File Path: /path/to/cellstats.tsv

Metadata Sheet

  • Description: Extended metadata file containing sample annotations and experimental conditions.
  • Format: Tab-separated values (.tsv)
  • Example File Path: /path/to/metadata.tsv

Outputs

Reported Outputs

  • Analysis Report HTML:
  • Description: Comprehensive interactive HTML report containing QC metrics, spatial visualizations, clustering results, and analysis summary
  • Format: .html
  • Example File Path: /output/sample_name.analysis_report.html
  • Visualization App: Web browser

  • Location: Output directory

  • Analysis RDS File:

  • Description: Processed spatial data object in R format containing filtered expression matrix, spatial coordinates, and metadata
  • Format: .rds
  • Example File Path: /output/sample_name.analysis.rds
  • Visualization App: R/RStudio, Seurat
  • Location: Output directory

Supporting Outputs

  • Processed Dataset Directory:
  • Description: Structured directory containing extracted and organized Xenium data files ready for analysis
  • Format: Directory structure with multiple file types (.csv, .parquet, .tif, .json)
  • Example File Path: /intermediate/sample_name_out/
  • Location: Intermediate processing directory

Associated Processes

References & Additional Documentation

  • Related Papers/links: 10x Genomics Xenium Platform Documentation
  • Workflow Diagram: High-resolution spatial transcriptomics processing with tissue preparation, probe hybridization, RCA amplification, imaging, and computational analysis