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Xenium Output Files at a Glance

Xenium Output Files at a Glance

The raw output data generated by the Xenium Onboard Analysis pipeline consists of decoded transcript counts and morphology images (also see Archiving Xenium data). These data reduce low-level internal image sensor data, preserving details needed to assess decoded transcript quality (learn more at Overview of Xenium Algorithms).

Raw output and other standard output files derived from them are included in the Xenium output directory for each selected region. These files are listed below and described in more detail on the Understanding Xenium Outputs page.

The following files are provided in the output directory. See the release notes for descriptions of output file changes in each software version.

File typeFile and descriptionRead in Xenium Explorer
Experiment fileexperiment.xenium: Experiment manifest file. Required
Interactive summaryanalysis_summary.html: Summary metrics, graphs, and images to QC your run data in HTML format.
Image filesmorphology.ome.tif: The 3D nuclei-stained (DAPI) morphology image in OME-TIFF format.
 morphology_focus/: A directory containing the multi-focus projection of morphology image(s) in a multi-file OME-TIFF format (2D). The directory will contain the nuclei DAPI stain image, as well as three additional stain images for Xenium outputs generated with the multimodal cell segmentation assay workflow.
Cell summarycells.csv.gz: Cell summary file.
 cells.parquet: Cell summary file in Parquet format.
Cell segmentation masks and Cell summary file in zipped Zarr format, only file that contains the nucleus and cell segmentation masks and boundaries used for transcript assignment.
Cell boundary polygonscell_boundaries.csv.gz: Cell boundary file.
 cell_boundaries.parquet: Cell boundary file in Parquet format.
Nucleus boundary polygonsnucleus_boundaries.csv.gz: Nucleus boundary file.
 nucleus_boundaries.parquet: Nucleus boundary file in Parquet format.
Transcript datatranscripts.parquet: Transcripts data in Parquet format. Transcript data in zipped Zarr format.
Cell-feature matrixcell_feature_matrix/: Directory of the cell-feature matrix files in Market Exchange format.
 cell_feature_matrix.h5: Cell-feature matrix file in HDF5 format. Cell-feature matrix file in zipped Zarr format.
Metric summarymetrics_summary.csv: Summary of key metrics.
Secondary analysisanalysis/: Directory of secondary analysis results. Secondary analysis outputs in zipped Zarr format.
Gene panelgene_panel.json: Copy of input gene panel file.
Auxiliary data (aux_outputs/)
  • morphology_fov_locations.json: Field of view (FOV) name and position information (in microns).
  • overview_scan_fov_locations.json: FOV name and position information (in pixels).
  • per_cycle_channel_images/: Directory of downsampled RNA image files in TIFF format from each cycle and channel.
  • overview_scan.png: Full resolution image of entire slide sample.
  • background_qc_images/: Directory of autofluorescence images in TIFF format that correspond to morphology_focus/ images if generated.