The 10x Explorer software uses the files listed in the tables below to visualize Atera Onboard Analysis and Xenium Onboard Analysis datasets.
The experiment manifest file is required to open any dataset, as it tells 10x Explorer where to find the files needed to fully explore image, cell segmentation, transcript, and secondary analysis results.
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 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 tables below).
- At least one of the morphology image files (
ome.tif) must be available in the directory to open the dataset. - Datasets can be opened in 10x Explorer even if the remaining
ome.tif,.zarr.zip, or.htmlfiles are missing from the output bundle, however functionality will be limited to the files that are present.
To view 10x Genomics public data in 10x Explorer, download and unzip the Atera Onboard Analysis or Xenium Onboard Analysis Output Bundle file.
10x Explorer expects the following output bundle files in one directory to open an Atera Onboard Analysis v1.0 Atera Gene Expression dataset:
└── outs
├── analysis_summary_<INST_SN>_<SLIDE_NAME>_<ROI_NAME>.html
├── binned_transcripts.zarr.zip
├── cell_feature_matrix.zarr.zip
├── cells.zarr.zip
├── csc_cell_feature_matrix.zarr.zip
├── experiment.spatial
├── panel_config.json
├── morphology_2d
│ ├── ch0000_dapi.ome.tif
│ ├── ch0001_atp1a1_e-cadherin_cd45.ome.tif
│ ├── ch0002_18s.ome.tif
│ └── ch0003_alphaSMA_vimentin.ome.tif
├── morphology_3d/ch0000_dapi_3d.ome.tif
└── transcripts.zarr.zip
These Atera Onboard Analysis files are read by 10x Explorer (see Understanding Atera Outputs for all output file descriptions):
| 10x Explorer function | File and description |
|---|---|
| Define experiment | experiment.spatial: A small JSON manifest file that includes experiment metadata and references to files in the Atera Onboard Analysis output folder.Required to open any experiment in 10x Explorer. |
| View 3D morphology image | morphology_3d/ch0000_dapi_3d.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. |
| View 2D focus image | morphology_2d/[channel]_[marker name].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 and interior cell images, as well as cell boundary and interior protein stain images if optional Atera Cell Segmentation Staining Reagents are used. |
| View cell segmentation polygons | cells.zarr.zip: The cell summary file in zipped Zarr format that contains the nucleus and cell segmentation masks and boundaries used for transcript assignment. 10x Explorer displays the cell segmentation polygons defined by this file. |
| View transcript location and density information | transcripts.zarr.zip: Transcript data in zipped Zarr format for viewing transcripts as points. |
binned_transcripts.zarr.zip: Binned transcript data in zipped Zarr format for viewing transcripts as bins in a density map. | |
| View transcripts per cell and secondary analysis results | cell_feature_matrix.zarr.zip: The cell-feature matrix file in zipped Zarr format, including secondary analysis (cell group clusters). 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. |
csc_cell_feature_matrix.zarr.zip: Transposed cell-feature matrix file in zipped Zarr format for more efficient visualization of transcripts per cell. | |
| View summary information | analysis_summary_<INST_SN>_<SLIDE_NAME>_<ROI_NAME>.html: Summary metrics and plots to QC your run data in HTML format. |
10x Explorer expects the output bundle files in one directory to open a Xenium Onboard Analysis dataset. For example, these files are expected for a v4.0 Xenium In Situ Gene Expression with Cell Segmentation Staining dataset:
└── outs
├── analysis.zarr.zip
├── analysis_summary.html
├── cell_feature_matrix.zarr.zip
├── cells.zarr.zip
├── experiment.xenium
├── gene_panel.json
├── morphology_focus
│ ├── ch0000_dapi.ome.tif
│ ├── ch0001_atp1a1_e-cadherin_cd45.ome.tif
│ ├── ch0002_18s.ome.tif
│ └── ch0003_alphaSMA_vimentin.ome.tif
├── morphology.ome.tif
└── transcripts.zarr.zip
These Xenium Onboard Analysis outputs are read by 10x Explorer (see Understanding Xenium Outputs for all output file descriptions):
| 10x Explorer function | File and description |
|---|---|
| Define experiment | experiment.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 10x Explorer. |
| View 3D morphology image | morphology.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. |
| View 2D focus image | morphology_focus/[channel]_[marker name].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 additional stain images for Xenium outputs generated with the multimodal cell segmentation or Xenium Protein assay workflows.This directory is provided in the output bundle in Xenium Onboard Analysis v2.0 and later. Files were previously called morphology_focus_xxxx.ome.tif. |
morphology_focus.ome.tif: Single best-focus Z-plane of the morphology image.This file is generated in Xenium Onboard Analysis v1.0 - 1.9. | |
| View 2D MIP image | morphology_mip.ome.tif: Maximum intensity projection (MIP) of the morphology image.This file is generated in Xenium Onboard Analysis v1.0 - 1.9. |
| View cell segmentation polygons | cells.zarr.zip: The cell summary file in zipped Zarr format that contains the nucleus and cell segmentation masks and boundaries used for transcript assignment. 10x Explorer displays the cell segmentation polygons defined by this file. |
| View transcript assignment | transcripts.zarr.zip: Transcript data in zipped Zarr format for visualization in 10x 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. It also includes protein mean intensity data for Xenium Protein datasets. | |
| View secondary analysis | analysis.zarr.zip: The secondary analysis outputs in zipped Zarr format, which includes cell clustering results. |
| View summary information | analysis_summary.html: Summary metrics and plots to QC your run data in HTML format. |
10x Explorer can also read the following input files, which are not part of either the Atera Onboard Analysis or Xenium Onboard Analysis output bundles.
| 10x Explorer function | File and description |
|---|---|
| View post-instrument images | Import post-instrument 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-instrument image generated with and downloaded from 10x Explorer. Reimport file via the image alignment workflow. | |
keypoints.csv: The keypoints coordinates corresponding to an aligned post-instrument image generated with and downloaded from 10x Explorer. Reimport file via the image alignment workflow. | |
| Custom gene groups CSV | Import custom gene groups to view transcript data. |
| Custom cell groups CSV | Import custom cell groups to view cell data. |
| Custom cell metrics CSV | Import custom cell metrics to view cell data. |
| Custom annotations | Import annotation polygons for regions of interest. |