The experiment.xenium file is an output from the Xenium Onboard Analysis pipeline. The metadata fields in this file are described below:
| Field | Description |
|---|---|
major_version | Indicates major version of analysis output file formats read by Xenium Explorer |
minor_version | Indicates minor version of analysis output file formats read by Xenium Explorer |
patch_version | Patch version of analysis output file formats read by Xenium Explorer |
run_name | User-specified Run Name entered on instrument |
run_start_time | Instrument run start time |
region_name | User-specified name for region selected on instrument |
preservation_method | User-specified sample preservation method |
num_cells | Cells detected by Xenium Onboard Analysis pipeline |
transcripts_per_cell | Median transcripts per cell calculated by Xenium Onboard Analysis pipeline |
transcripts_per_100um | Transcripts per 100 µm2 calculated by Xenium Onboard Analysis pipeline |
region_area | Total area of imaged field of views (FOVs) |
total_cell_area | Summed area of detected cells |
thickness_of_high_quality_decoded_transcripts | Width in Z of high-quality transcripts measured in microns |
non_zero_matrix_entries | Number of nonzero entries in the sparse CSC cell-feature matrix in the cell_feature_matrix.zarr.zip file |
nuclear_transcripts_per_100um | Number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area |
num_transcripts | Total number of transcripts including low-quality transcripts |
num_transcripts_high_quality | Total high quality decoded transcripts (≥ Q20) |
fraction_transcripts_assigned | Percent of high-quality transcripts that are found within cells |
segmented_cell_stain_frac | Sum of segmented_cell_boundary_frac and segmented_cell_interior_frac |
segmented_cell_boundary_frac | Number and percent of cells where the cell segmentation boundary is derived from the boundary stain |
segmented_cell_interior_frac | Number and percent of cells where the boundary is from expansion of the nucleus using interior stain information |
segmented_cell_nuc_expansion_frac | Number and percent of cells where the boundary is an isotropic expansion from the nucleus boundary |
imported_cell_frac | Fraction of cells that were imported by Xenium Ranger import-segmentation |
cassette_name | User-specified Xenium Cassette Name entered on instrument |
slide_id | User-specified Xenium Slide ID entered on instrument |
panel_type | Panel type specified by the gene_panel.json file ("Predesigned", "custom", or "add_on") |
panel_design_id | Panel design ID specified by panel selection on instrument (additionally panel_predesigned_id is included for add-on custom panel designs) |
panel_designer_version | Xenium Panel Designer software version used for the custom panel design |
panel_name | Panel name specified by panel selection on instrument |
panel_organism | Sample organism specified by selected gene panel |
panel_tissue_type | User-specified tissue type selected on instrument |
panel_num_targets_predesigned | Number of gene targets from the pre-designed gene panel |
panel_num_targets_custom | Number of gene targets from add-on custom panel if included in panel design |
chemistry_version | Assay chemistry specified by the gene_panel.json file ("v1" = Xenium v1, "v2" = Xenium Prime) |
pixel_size | Pixel size in the morphology.ome.tif image file (in µm) |
instrument_sn | Xenium Analyzer instrument serial number |
instrument_sw_version | Version of the Xenium Analyzer firmware used during analysis run |
analysis_sw_version | Version of Xenium Onboard Analysis pipeline used to analyze data |
analysis_uuid | Instrument metadata |
experiment_uuid | Instrument metadata |
cassette_uuid | Instrument metadata |
roi_uuid | Instrument metadata |
z_step_size | Z-step size (in µm) used for subsampling the morphology.ome.tif image Z-stacks |
well_uuid | Instrument metadata |
calibration_uuid | Instrument metadata |
images | Specifies the file paths to the morphology image files; used by Xenium Explorer to find input files |
xenium_explorer_files | Specifies the file paths to transcript, cell, secondary analysis, and analysis summary files; used by Xenium Explorer to find input files |
segmentation_stain | Specifies the stain method selected on instrument for cell segmentation ("Xenium Multi-Tissue Stain" or "Nuclei (DAPI)"). |
xenium_ranger | If the data was reanalyzed with Xenium Ranger, this section specifies the run_id, Xenium Ranger version, and commands used to analyze the data. |
The major_version field in this file indicates when there are changes to Xenium Onboard Analysis (XOA) output file formats that affect forwards-compatibility with other software.
Updates to major_version are associated with new releases of the XOA software on the Xenium Analyzer (XA) instrument. This format version is used by Xenium Explorer (XE) and Xenium Ranger (XR) to determine input file compatibility across the Xenium software suite. This table summarizes when file format major versions were introduced by XOA software version.
| XOA version | experiment.xenium major version |
|---|---|
| XOA v3.1 | 5.1 † |
| XOA v3.0 | 5.0 |
| XOA v2.0 | 4.0 |
| XOA v1.7 - v1.9 | 3.0 |
| XOA v1.6 | 2.0.2 |
| XOA v1.5 | 2.0.1 |
| XOA v1.3 - v1.4 | 2.0 |
| XOA v1.2 | 1.1 |
| XOA v1.0 - v1.1 | (no version fields) |
† Reanalysis with Xenium Ranger v3.0 generates outputs that align with the XA/XOA v3.1 output format and experiment.xenium major version v5.1.