10x Genomics Support/Xenium Explorer/Tutorials/

Xenium Explorer Input Files

The Xenium Onboard Analysis output files listed below are needed to use all Xenium Explorer features (see Understanding Xenium Outputs for all output file descriptions). The experiment.xenium file is required to open any dataset in Xenium Explorer. The remaining ome.tif and zarr.zip files are needed to fully explore image, cell segmentation, and transcript information. The analysis_summary.html is needed to view the summary file in Xenium Explorer.

The .xenium manifest file tells Xenium Explorer where to find these files. To properly open a dataset:

  • Files must be saved in the same directory path as the manifest file (e.g., default file structure of the Xenium Onboard Analysis output directory), unless file paths have been modified in the manifest file
  • File names must match what is specified in the manifest file (default file names shown in table below).
  • At least one of the morphology image files (ome.tif) must be available in the directory.
  • Datasets can be opened in Xenium Explorer even if any of the ome.tif, .zarr.zip, or .html files are missing from the output bundle, however functionality will be limited to the files that are present.
Important
To view 10x Genomics public data in Xenium Explorer, download and unzip the Xenium Output Bundle file or the Xenium Explorer subset if available.
Xenium Explorer functionFile and description
Define experimentexperiment.xenium: A small JSON manifest file that includes experiment metadata and references to files in the Xenium Onboard Analysis output folder.

Required to open any experiment in Xenium Explorer.
View 3D morphology imagemorphology.ome.tif: The tissue morphology image is the nuclei-stained (DAPI) image in OME-TIFF format. This file includes a pyramid of resolutions and tiled chunks of image data for efficient interactive image viewing.

Required in XE v1.0 - 1.1, optional in XE v1.2 and later.
View 2D autofocus imagemorphology_focus/morphology_focus_xxxx.ome.tif: A directory containing the multi-focus projection of morphology image(s) in a multi-file OME-TIFF format. 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.

This directory is provided in the output bundle starting in XOA v2.0.
morphology_focus.ome.tif: Single best-focus Z-plane of the morphology image.

This file is generated in XOA v1.0 - 1.9.
View 2D MIP imagemorphology_mip.ome.tif: Maximum intensity projection (MIP) of the morphology image.

This file is generated in XOA v1.0 - 1.9.
View cell segmentation polygonscells.zarr.zip: The cell summary file in zipped Zarr format that contains the nucleus and cell segmentation masks and boundaries used for transcript assignment. Xenium Explorer displays the cell segmentation polygons defined by this file.
View transcript assignmenttranscripts.zarr.zip: Transcript data in zipped Zarr format for visualization in Xenium Explorer.
cell_feature_matrix.zarr.zip: The cell-feature matrix file in zipped Zarr format. It contains the transcript count for each gene that was observed inside the segmentation mask of each cell. By default, it only includes transcripts that pass the default Q-Score threshold of Q20.
View secondary analysisanalysis.zarr.zip: The secondary analysis outputs in zipped Zarr format, which includes cell clustering results.
View summary informationanalysis_summary.html: Summary metrics and plots to QC your run data in HTML format.
View post-Xenium images (not part of Xenium Onboard Analysis output bundle)Import post-Xenium H&E and/or IF images in a pyramidal, tiled, OME-TIFF format (see image alignment tutorial for details).
imagealignment.csv: The affine transformation matrix values corresponding to an aligned post-Xenium image generated with and downloaded from Xenium Explorer. Reimport file via the image alignment workflow.
keypoints.csv: The keypoints coordinates corresponding to an aligned post-Xenium image generated with and downloaded from Xenium Explorer. Reimport file via the image alignment workflow.