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).
Important
See what's new in the Xenium Onboard Analysis software pipeline. Click here to read the release notes.
| File type | File and description | Read in 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 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 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 nuclei 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.csv.gz: Transcripts data file | |
transcripts.parquet: Transcripts data in Parquet format | ||
transcripts.zarr.zip: Transcript data in zipped Zarr format | ||
| Cell-feature matrix | cell_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 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 | |
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 channeloverview_scan.png: Full resolution image of entire slide sample |