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. For quick reference, these files are listed in the tables below.
All output files are described in more detail on the following pages:
The following files are provided in the output directory. See the release notes for descriptions of output file changes in each software version.
| File type | File and description | Read by Xenium Explorer |
|---|---|---|
| Experiment file | experiment.xenium: Experiment manifest file. | Required |
| Interactive summary | analysis_summary.html: Summary metrics, graphs, and images to QC your run data in HTML format. | |
| Image files | morphology.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 summary | cells.csv.gz: Cell summary file. | |
cells.parquet: Cell summary file in Parquet format. | ||
| Cell segmentation masks and polygons | cells.zarr.zip: 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 polygons | cell_boundaries.csv.gz: Cell boundary file. | |
cell_boundaries.parquet: Cell boundary file in Parquet format. | ||
| Nucleus boundary polygons | nucleus_boundaries.csv.gz: Nucleus boundary file. | |
nucleus_boundaries.parquet: Nucleus boundary file in Parquet format. | ||
| Transcript data | transcripts.parquet: Transcripts data in Parquet format. | |
transcripts.zarr.zip: Transcript data in zipped Zarr format. | ||
| Cell-feature matrix | cell_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.zarr.zip: Cell-feature matrix file in zipped Zarr format. | ||
| Metric summary | metrics_summary.csv: Summary of key metrics. | |
| Secondary analysis | analysis/: Directory of secondary analysis results. | |
analysis.zarr.zip: Secondary analysis outputs in zipped Zarr format. | ||
| Gene panel | gene_panel.json: Copy of input gene panel file. | |
| Protein panel | protein_panel.json: Copy of instrument-generated protein panel file for Xenium In Situ Gene and Protein Expression with Cell Segmentation Staining assay. (New in XOA v4.0) |
The auxiliary data outputs (aux_outputs/) are listed below. The JSON, TIFF, and PNG files are not ready by Xenium Explorer. The morphology_focus_qc_masks can be imported to Xenium Explorer.
| File name | Description |
|---|---|
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 (downsampled, TIFF format) that are subtracted from the raw stain images to produce the morphology_focus/ images if Cell Segmentation Staining or Xenium In Situ Gene and Protein Expression with Cell Segmentation Staining assay is used. |
morphology_focus_qc_masks/ | Directory of saturation QC mask image files in OME-TIFF format from each cycle and channel. They are 8-bit mask images where pixels have two possible values: 255 if extrapolated autofluorescence (using background images) is saturated and 0 if not. (New in XOA v4.0) |