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At a Glance: Xenium Output Files

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 (listed below and described in more detail here).

See what's new in the Xenium Onboard Analysis software pipeline. Click here to read the release notes.
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 nuclei-stained (DAPI) morphology image in OME-TIFF format
 morphology_focus.ome.tif: Single best-focus Z-plane of the morphology image
 morphology_mip.ome.tif: Maximum intensity projection (mip) of the morphology image
Cell summarycells.csv.gz: Cell summary file
 cells.parquet: Cell summary file in Parquet format
Cell segmentation masks and polygonscells.zarr.zip: Cell summary file in zipped Zarr format, only file that contains the nuclei 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.csv.gz: Transcripts data file
 transcripts.parquet: Transcripts data in Parquet format
 transcripts.zarr.zip: Transcript data in zipped Zarr format
Cell-feature matrixcell_feature_matrix/: Cell-feature matrix file in Market Exchange format
 cell_feature_matrix.h5: Cell-feature matrix file in HDF5 format
 cell_feature_matrix.zarr.zip: Cell-feature matrix file in zipped Zarr format
Metric summarymetrics_summary.csv: Summary of key metrics
Secondary analysisanalysis/: Directory of secondary analysis results
 analysis.zarr.zip: 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/: A folder containing downsampled RNA image files in TIFF format from each cycle and channel
  • overview_scan.png: Full resolution image of entire slide sample
  • Document Type

    Last Modified
    November 3, 2023