v1.2 (March 2023)

Output file changes

• Added field of view (FOV) information to transcripts output files:
  • Added fov_name column to transcripts.csv.gz and transcripts.parquet. FOV names use chessboard nomenclature.
  • Added aux_outputs/fov_locations.json file to Xenium output bundle. It contains the global coordinates for FOVs.
• Added versioning to experiment.xenium for file compatibility checking in Xenium Explorer.

General improvements

• Improved decoding algorithm to reduce FOV-to-FOV variation.
• Reduced FOV size to eliminate transcript quality roll-off. FOV demarcation (row x columns) changed from 28 x 19 to 33 x 19 FOVs. FOV size changed from 4240 x 2960 pixels to 3520 x 2960 pixels.

Bug fixes and miscellaneous changes

• "GEX" in panel names changed to "Gene Expression".
• Instrument metadata (calibration_uuid) added to experiment.xenium.

v1.1 (February 2023)

Output file changes

• “Blank Codeword” feature type in cell-feature matrix renamed to “Unassigned Codeword”.
• Added unassigned_codeword_counts column to cells.csv.gz and cells.parquet files.
• Increased chunk size of precomputed densities in transcripts.zarr for faster loading in Xenium Explorer.

General improvements

• Improved run time estimation accuracy.

Bug fixes and miscellaneous changes

• Fixed analysis_summary.html (Instrument software version field) and experiment.xenium (instrument_sw_version field) to show correct instrument software version.
• Based on additional experimental data, thresholds for high negative control probe rate warning and error alerts were increased from 2% to 4% and 5% to 10%, respectively, in the analysis_summary.html.
• Various styling improvements to analysis_summary.html.
• Minor bug fixes