The experiment.spatial file is an output from the Atera Onboard Analysis pipeline. The metadata fields in this file are described below, grouped by the fields pertaining to instrument run and panel configuration, analysis metrics, and output files.
| Field | Description |
|---|---|
major_version | Indicates major version of analysis output file formats. Used by other software to check compatibility. |
minor_version | Indicates minor version of analysis output file formats. Used by other software to check compatibility. |
run_name | User-specified analysis run name on instrument |
run_start_time | Instrument run start time |
slide_name | User-specified slide name on instrument |
slide_id | User-specified slide ID (optional) on instrument |
region_name | User-specified region name on instrument |
slide_type | Slide type used on instrument |
sample_type | User-specified sample preservation method |
panel_config | Specifies the name and ID of the panel configuration |
panel_[...] | For each panel in the panel configuration (possible fields: panel_WTA, panel_a, panel_c), specifies panel name, panel design ID, number of targets, organism, and tissue type |
total_num_targets | Total number of unique targets in the panel configuration |
segmentation_stain | The segmentation stain method ("atera_cell_segmentation_stains_v1" or "atera_dapi_18s_only_v1") |
chemistry_version | Assay chemistry specified by the panel_config.json file ("Atera v1") |
pixel_size | Pixel size in the morphology_3d/ch0000_dapi_3d.ome.tif image file (in µm) |
z_step_size | Z-step size (in µm) used for subsampling the morphology_3d/ch0000_dapi_3d.ome.tif image Z-stacks |
instrument_sn | Atera Instrument serial number |
instrument_sw_version | Version of the Atera Instrument firmware used during analysis run |
analysis_sw_version | Version of Atera Onboard Analysis pipeline used to analyze data |
analysis_uuid | Instrument metadata |
experiment_uuid | Instrument metadata |
cassette_uuid | Instrument metadata |
roi_uuid | Instrument metadata |
well_uuid | Instrument metadata |
calibration_uuid | Instrument metadata |
| Field | Description |
|---|---|
num_cells | Cells detected |
transcripts_per_cell | Median transcripts per cell |
genes_per_cell | Median genes per cell |
nuclear_transcripts_per_100um | Number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area |
transcripts_per_100um | Transcripts per 100 µm2 |
num_transcripts | Total number of transcripts including low-quality transcripts |
num_transcripts_high_quality | Total high quality decoded transcripts (≥ Q20) |
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 csc_cell_feature_matrix.zarr.zip file |
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 | Fraction of cells where the cell segmentation boundary is derived from the boundary stain |
segmented_cell_interior_frac | Fraction of cells where the boundary is from expansion of the nucleus using interior stain information |
segmented_cell_nuc_expansion_frac | Fraction of cells where the boundary is an isotropic expansion from the nucleus boundary |
segmented_nucleus_focus_frac | Fraction of nuclei that were segmented from focus images |
segmented_nucleus_focus_count | Number of nuclei that were segmented from focus images |
segmented_nucleus_zstack_frac | Fraction of nuclei that were segmented from Z-stack images |
segmented_nucleus_zstack_count | Number of nuclei that were segmented from Z-stack images |
cell_types | Cell type annotation categories (coarse, fine) |
| Field | Description |
|---|---|
images | Specifies the file paths to the 3D and 2D morphology image files |
explorer_files | Specifies the file paths to cell, transcript, cell-feature matrix and secondary analysis, and analysis summary files |
The major_version field in this file indicates when there are changes to Atera Onboard Analysis output file formats that affect forwards-compatibility with other software.
Updates to major_version are associated with new releases of the Atera Onboard Analysis software on the Atera Instrument. For example, this format version is used by 10x Explorer to determine input file compatibility across the 10x in situ software suite. This table summarizes when file format major versions were introduced by Atera Onboard Analysis software version.
| Atera Onboard Analysis version | experiment.spatial major version |
|---|---|
| v1.0 | 1.2 |