<LinkableSection id={"metadata"} title={"Field descriptions"}>

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.

</LinkableSection>

<LinkableSection id={"metadata-instr"} title={"Instrument run and panel config fields"} nested={true}>

| 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 &micro;m) 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                                                                                                                                                              |

</LinkableSection>

<LinkableSection id={"metadata-aoa"} title={"Atera Onboard Analysis pipeline metrics"} nested={true}>

| 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 &micro;m2                                                                                                                                                            |
| `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)                                                                                                                                     |


</LinkableSection>

<LinkableSection id={"metadata-explorer"} title={"Output fields read by 10x Explorer"} nested={true}>

| 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                                                                                       |

</LinkableSection>

<LinkableSection id={"expt-file-versions"} title={"Experiment file versions"}>

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 |

</LinkableSection>


Field descriptions

Instrument run and panel config fields

Atera Onboard Analysis pipeline metrics

Output fields read by 10x Explorer

Experiment file versions

Experiment File

Atera Instrument Software enables run set up, Atera Onboard Analysis data generation, and data egress.

Atera Onboard Analysis

Atera

Gene Expression

Atera Experiment File Metadata and Versions

<LinkableSection id={"decoding-metric-calc"} title={"Negative control metrics"}>

The [Atera Onboard Analysis output files](/support/software/atera-onboard-analysis/latest/analysis/output-understanding-outputs) `analysis_summary.html` and `metrics_summary.csv` report negative control metrics.

The "Negative control probe counts per control per cell" metric is derived first from calculating the absolute number of negative control probe counts and then calculating the metric per control probe per cell. The "Estimated number of false positive transcripts per cell" is derived from this metric. Derived values may differ slightly from those reported in summary outputs due to using rounded values.

They are calculated using the following inputs:

- Total high quality decoded transcripts: displayed on the Summary and Decoding tabs, includes genes (Q-Score ≥ 20) and negative controls
- Percent of transcripts within cells: displayed on the Cell Segmentation tab
- **Adjusted negative control probe rate**: displayed on the Decoding tab
- Number of target genes: the sum of genes in the pre-designed panel and any custom genes, displayed on the Summary tab
- **Number of negative control probes in the panel**: in Atera v1, the pre-designed WTA panel contains 81 negative control targets and Select contains 40.
- Number of cells detected: hero metric on the Summary tab

1. The _Negative control probe count_ is calculated as:

   $$ \footnotesize{\text{Q20 decoded transcripts in cells}\times{\text{Adjusted negative control probe rate}}\times{\frac{\text{Number of negative control probes}}{\text{Number of target genes}}}} $$

   where _Q20 decoded transcripts in cells_ is calculated as:

   $$ \footnotesize{\text{Total high quality decoded transcripts}\times{\text{Percent of transcripts within cells}}} $$

2. The `Negative control probe count per control per cell` is then calculated as:

   $$ \footnotesize{{\text{Negative control probe count}}\div{\text{Number of negative control probes}}\div{\text{Number of cells detected}}} $$

3. The `Estimated number of false positive transcripts per cell` is calculated as:

   $$ \footnotesize{{\text{Negative control probe counts per control per cell}}\times{\text{Number of target genes}}} $$

The calculations for "Genomic control probe counts per control per cell" and "Estimated number of false positive transcripts per cell including genomic counts" are analogous to the calculations shown above.

The inputs are:

- Total high quality decoded transcripts
- Percent of transcripts within cells
- **Adjusted genomic control probe rate**
- Number of target genes
- **Number of genomic control probes in the panel** (Pre-designed WTA: 61, Select: 20)
- Number of cells detected

</LinkableSection>


Negative control metrics

Metric Calculations

Calculating Negative Control Metrics

Atera Instrument Software enables run set up through data egress on the Atera Instrument, including simultaneous on-instrument data analysis by the Atera Onboard Analysis pipeline.

Overview

Getting Started

Instrument Software

Analysis

Algorithms

Example Datasets

Release Notes

Advanced

Analysis Guides

Atera Instrument Software

Storing Atera raw data for reanalysis or grant requirements.

Archiving Atera Data

A quick reference table of Atera Onboard Analysis pipeline output files.

Outputs at a Glance

Overview of Atera Onboard Analysis pipeline output bundle structure and files.

Atera Output Bundle

Overview of interactive Atera HTML summary output files.

Interactive Summaries

Overview of Zarr-formatted cell and transcript output files.

Cells and Transcripts

What is Atera Instrument Software?

View the latest updates to Atera Instrument Software.

Browse Q&As from the 10x Genomics support team.

A collection of introductions, tutorials, and blogs for data analysis beyond 10x Genomics software.