v0.21.0

[0.21.0] - 2025-06-24

Added

• Added component denoising functionality to be invoked as pixelator single-cell-pna denoise.
  Denoising removes nodes from markers that are overrepresented in the 1-core layer of a cell graph which suggests that they are caused by bleed-over from other cells.
• Added the proxiome-immuno-156-FMC63 panel, which includes all the markers from the proxiome-immuno-155 panel, but with the addition of the FMC63 marker.
• Support for python 3.12. The container builds for pixelator will use python 3.12 from this point.
• Added molecules_post_umi_collision_removal and reads_post_umi_collision_removal to the graph report file.

Changed

• The proximity data will no longer be reported for markers with fewer than 10 molecules in the cell.
• Two columns, marker_1_freq and marker_2_freq, have been added to the proximity data to indicate the respective marker frequencies.
• Panel files no longer allow _ as a character in the marker ids, since this causes problems with Seurat in R in downstream analysis.

Fixed

• Pixelator can now handle sample names starting with a number for PNA data.
• Work around a bug in pyarrow that could cause the pixelator single-cell-pna demux to generate invalid molecule embeddings for very large input files.
• Update tau metric information after denoising components.
• Fix the number of input reads and molecules in the graph report to correspond to the raw counts and add the number of reads and molecules after UMI collision removal as separate entries in the report.