The raw output data generated by the Xenium Onboard Analysis pipeline consists of decoded transcript counts and morphology images. 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).
For more detailed descriptions, go to the Understanding Xenium Outputs page.
| File type | File and description | Read in Xenium Explorer |
|---|---|---|
| Secondary analysis | analysis/: Directory of secondary analysis results | |
analysis.zarr.zip: Secondary analysis outputs in zipped Zarr format | ||
| Interactive summary | analysis_summary.html: Summary metrics and graphs to QC your run data in HTML format | |
Auxiliary outputs subfolder (aux_outputs/) | fov_locations.json: Field of view (FOV) name and position information | |
| Cell boundary | cell_boundaries.csv.gz: Cell boundary file | |
cell_boundaries.parquet: Cell boundary file in Parquet 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 | ||
| Cell summary | cells.csv.gz: Cell summary file | |
cells.parquet: Cell summary file in Parquet format | ||
| Cell segmentation | cells.zarr.zip: Cell summary file in zipped Zarr format, which also contains the segmentation masks and boundaries for nuclei and cells | |
| Experiment file | experiment.xenium: Experiment manifest file | Required |
| Gene panel | gene_panel.json: Copy of input gene panel file | |
| Metric summary | metrics_summary.csv: Summary of key metrics | |
| Image files | morphology.ome.tif: The nuclei-stained (DAPI) morphology image in OME-TIFF format | Required |
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 | ||
| Nucleus boundary | 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 |