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Spatial Data Analysis Specifications

Process Details

  • Name: Spatial Data Analysis
  • Process UUID: dy6r4mdcvadgjaiqo0qefxs1u0jkoy
  • Process Group: SingleCell

Overview

This process performs comprehensive spatial transcriptomics data analysis using Xenium spatial data. The analysis includes quality control filtering, spatial visualization, and statistical analysis of spatially resolved gene expression data. The process generates both processed data objects and detailed analytical reports for spatial transcriptomics experiments.

This process is implemented in Bash, which invokes an R script for spatial data analysis using Seurat.

Key Functionality

  • Quality Control Filtering: Applies quantile-based thresholds to filter cells based on transcript molecule counts and gene detection metrics
  • Spatial Data Processing: Processes Xenium spatial transcriptomics output data including expression matrices and spatial coordinates
  • Boundary Visualization: Supports multiple segmentation options (cell, nucleus, or none) for spatial boundary plotting and visualization
  • Report Generation: Creates comprehensive HTML reports with spatial plots, quality metrics, and analysis results

Input/Output Specification

Inputs

Required Inputs

  • Input Directory

    • Description: Directory containing Xenium spatial transcriptomics output files
    • Format: Directory

  • Cell Statistics File

    • Description: TSV file containing cell-level statistics and quality metrics
    • Format: TSV

  • Metadata Sheet

    • Description: TSV file containing sample metadata and experimental annotations
    • Format: TSV

Outputs

  • Analysis Object

    • Description: Processed spatial transcriptomics data object containing filtered expression data, spatial coordinates, and analysis results
    • Format: RDS

  • Analysis Report

    • Description: Comprehensive HTML report with spatial visualizations, quality control metrics, and analysis summary
    • Format: HTML

Parameters & Settings

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

  • Min threshold

    • Description: Cutoff Quantile for minimum number of unique transcript molecules and genes in a cell
    • Default value: 0.01

  • Max threshold

    • Description: Cutoff Quantile for maximum number of unique transcript molecules and genes in a cell
    • Default value: 0.99

  • Segmentations for boundary

    • Description: Xenium Segementations to be used for Boundry while plotting
    • Available options: cell, nucleus (default), none

References & Resources

  • Tool Documentation: Contact the team for details on Final_Report.Rmd
  • Related Papers: Hao, Y., Hao, S., Andersen-Nissen, E., Mauck, W.M., Zheng, S., Butler, A., Lee, M.J., Wilk, A.J., Darby, C., Zager, M., Hoffman, P., Stoeckius, M., Papalexi, E., Mimitou, E.P., Jain, J., Srivastava, A., Stuart, T., Fleming, L.M., Yeung, B., Rogers, A.J., McElrath, J.M., Blish, C.A., Gottardo, R., Smibert, P., Satija, R. (2021). Integrated analysis of multimodal single-cell data. Cell, 184(13), 3573-3587.e29. https://doi.org/10.1016/j.cell.2021.04.048