The Atera Onboard Analysis pipeline generates several files containing information about cells and transcripts in Zarr v2 format in the output bundle. The Zarr format saves large amounts of data by storing them as compressed chunks of N-dimensional arrays.

10x Explorer reads these files to display cell segmentation, transcript assignment, and secondary analysis clustering results on the stained tissue morphology images.

In the pages below, we describe the specifications for each Zarr output file, including group arrays and attributes associated with each file.

The transcripts file contains all decoded transcripts. The binned transcript, cell-feature matrix, and secondary analyses only include transcripts with a Q-Score ≥ 20.