The software involved in producing Atera data include the following:

• Atera Instrument software: Versioned on-instrument software responsible for run set up through data egress, including Atera Onboard Analysis. Atera Onboard Analysis is the versioned on-instrument pipeline responsible for processing data and generating the final output bundle. See the Atera Instrument User Guide (CG001673) for all details on preparing, running, and egressing data from the instrument.
• 10x Cloud Instrument Manager: Cloud-based software responsible for instrument monitoring and real-time status updates (instrument registration to the 10x Cloud is required).

On this website, you will find documentation for Atera Instrument run time estimation, run status monitoring, and Atera Onboard Analysis outputs and algorithms. Atera Instrument and Atera Onboard Analysis software version updates are tracked in the release notes page.

The Atera Instrument's raw output data consists of decoded transcript counts and morphology images (see Archiving Atera Data page). The Atera Onboard Analysis output bundle includes these raw outputs, as well as other standard output files derived from them, for each region selected on the instrument.

Atera Instrument software supports data generation and analysis of samples prepared with the Atera Gene Expression workflow.

The Atera Instrument protocol performs nuclei and interior cell staining and imaging by default. If the optional Atera Cell Segmentation Staining Reagents kit (PN-1001146) is used in assay preparation, boundary and interior protein stain images are also acquired on-instrument and used for cell segmentation. This option affects the algorithms that are used and the outputs produced by the Atera Onboard Analysis pipeline.

Atera Onboard Analysis outputs can be visualized in 10x Explorer.