Xenium

note

Spatial transcriptomics platform from 10x Genomics that provides subcellular resolution.

https://www.10xgenomics.com/platforms/xenium

Xenium is a spatial transcriptomics platform from 10x Genomics that provides subcellular resolution.

note

This module provides basic quality metrics from the Xenium pipeline (total transcripts, cells detected, transcript assignment rates, and median genes per cell).

For advanced visualizations including:

• Transcript quality distributions by gene category
• Cell and nucleus area distributions
• Field-of-view quality plots
• Segmentation method breakdown
• Transcripts per gene distributions

Install the multiqc-xenium-extra plugin:

pip install multiqc multiqc-xenium-extra

The plugin automatically adjusts the log filesize limit to parse large Xenium files (.parquet and .h5), so you don't need to manually configure log_filesize_limit in your MultiQC config when using the plugin.

The MultiQC module is tested with outputs from xenium-3.x, older versions of xenium output are not supported and may even cause MultiQC to crash (see https://github.com/MultiQC/MultiQC/issues/3344).

File search patterns

xenium/experiment:
  fn: experiment.xenium
  num_lines: 50
xenium/metrics:
  contents: num_cells_detected
  fn: metrics_summary.csv
  num_lines: 5