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

Parsing huge files is not an intended MultiQC usage. By default, MultiQC will ignore the *.parquet files as they are gigabyte-sized. To enable parsing those, make sure to have this line in your config:

log_filesize_limit: 5000000000 # 5GB

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/cell_feature_matrix:
  fn: cell_feature_matrix.h5
xenium/cells:
  fn: cells.parquet
xenium/experiment:
  fn: experiment.xenium
  num_lines: 50
xenium/metrics:
  contents: num_cells_detected
  fn: metrics_summary.csv
  num_lines: 5
xenium/transcripts:
  fn: transcripts.parquet