For quick reference, the Atera Onboard Analysis output bundle files are listed in the table below. All output files are described in more detail on the Understanding Atera Outputs page. Updates to output files are tracked in the release notes for each software version.
| File type | File and description |
|---|---|
| Experiment file | experiment.spatial: Experiment manifest file in JSON format. |
| Interactive summary | analysis_summary_<INST_SN>_<SLIDE_NAME>_<ROI_NAME>.html: Summary metrics, graphs, and images to QC your run data in HTML format. Filename includes instrument serial number (SN), slide name, and region of interest (ROI) name. |
| Image-related files | morphology_3d/ch0000_dapi_3d.ome.tif: The 3D nuclei-stained (DAPI) morphology image in OME-TIFF format. |
morphology_2d/: A directory containing the multi-focus projection of morphology images 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. | |
overview_scan.png: Full resolution image of entire slide sample in PNG format. | |
morphology_fov_locations.json: Field of view (FOV) name and position information (in microns) in JSON format. | |
overview_scan_fov_locations.json: FOV name and position information (in pixels) in JSON format. | |
qc_images.html: Downsampled fluorescent images per cycle per channel in HTML format for troubleshooting sample quality issues. | |
| Transcript data | transcripts.zarr.zip: Transcript data in zipped Zarr format. |
binned_transcripts.zarr.zip: Binned transcript data in zipped Zarr format. This file is primarily used for visualizing transcript density by bins (e.g., in 10x Explorer). | |
| Cell segmentation masks and polygons | cells.zarr.zip: Cell segmentation file in zipped Zarr format. It contains the nucleus and cell segmentation masks and boundaries used for transcript assignment. |
| Cell-feature matrix | cell_feature_matrix.zarr.zip: Cell-feature matrix file in zipped AnnData Zarr format with cell summary and secondary analysis annotations. |
csc_cell_feature_matrix.zarr.zip: Transposed cell-feature matrix file in zipped Zarr format. This file is primarily used for more efficient visualization of the cell-feature matrix data (e.g., in 10x Explorer). | |
| Differential gene expression results | diffexp_genes/: Directory of differentially expressed gene analysis results in CSV format. |
| Metric summary | metrics_summary_<INST_SN>_<SLIDE_NAME>_<ROI_NAME>.csv: Summary of key metrics and metadata in CSV format. Filename includes instrument serial number (SN), slide name, and region of interest (ROI) name. |
| Panel configuration | panel_config.json: Copy of input panel configuration file uploaded to the Atera Instrument in JSON format. |