0.29.0

[0.29.0] - 2026-06-15

Added

• annotate_cells method to determine cell-types using another given set of pre-annotated cells.
• proxiome-v2-immuno-155-v2.0 panels (including panels for FLAG, FMC63 and G4S add ons to the immuno-155 base panel)
• Expose coarsened_pmds_3d (and other supported layout algorithms) on the single-cell-pna layout CLI, and make coarsened_pmds_3d the default.

Changed

• Switch sample calling evaluation metric to hash enrichment factor instead of hash purity.
• Reduce memory usage in pna_edgelist_to_anndata by restricting duckdb queries to 512 components at a time.

Fixed

• Always route DuckDB spill files to a local temp directory (PIXELATOR_DUCKDB_TEMP_DIR or /tmp)
  instead of next to the .pxl database file. This prevents denoise, component filtering and other
  commands from spilling onto networked filesystems (e.g. to S3 when running the pipeline in the cloud)
  where the .pxl may live.
• Fix the prerelease panel naming, rename proxiome-v2-immuno-155-v2.0 to proxiome-v2-immuno-155-prerelease.

0.28.0

[0.28.0] - 2026-06-03

Added

• coarsened_pmds_layout method for more performant cell layout computation

Fixed

• Performance regression (introduced in 0.27.1) in the graph command, where memory usage became
  extremely high towards the final stages of the process
• Fix rename panel files to reflect current version

0.27.2

[0.27.2] - 2026-05-29

Fixed

• Fix proxiome-v2 panel major version, from 1 to 2.

0.27.1

[0.27.1] - 2026-05-27

Added

• Add FMC63 proxiome-v2 panel

Fixed

• Fix full name of CD45RO in the proxiome-v1 and proxiome-v2 panel files.
• Fix CD298 annotation in the proxiome-v2 panel files.
• Propagate the demux --mismatches cli argument to correct_marker_barcodes (was using default i.e. 1)
• Follow uv.lock when building docker containers

0.27.0

[0.27.0] - 2026-05-22

Added

• Two new denoising methods to pixelator single-cell-pna denoise:
  • Adaptive Core Denoising (ACE) denoising: removes peripheral-like nodes around the graph core.
  • Partial Least Squares (PLS) denoising: filters nodes using PLS components associated with coreness.
• Automatically bump panel patch version when possible, when creating an reading Anndata object.

Changed

• When parsing panel files, trailing commas in the header will now give a warning and ignore the trailing commas,
  instead of raising an error.

Removed

• Remove the report command for both PNA and MPX.

Parameters

• pixelator single-cell-pna denoise

Old parameter	New parameter
	--run-ace-denoising
	--ace-k
	--ace-max-k-core
	--ace-no-select-lcc
	--one-core-ratio-threshold
	--pval-threshold
	--inflate-factor
	--run-pls-denoising
	--pls-ncomp
	--pls-model-k
	--pls-pred-k
	--pls-use-weights / --pls-no-weights
	--pls-normalization
	--pls-residualize
	--pls-component-p-threshold
	--pls-min-coreness-correlation
	--pls-score-threshold

Note

Parameter has been updated if both old and new parameter information is present.
Parameter has been added if just the new parameter information is present.
Parameter has been removed if new parameter information isn't present.

0.26.0

[0.26.0] - 2026-05-04

Important changes

The assay and panel names have been migrated to the new naming scheme.

Use proxiome-v1 instead of pna-2 for the --design command-line argument.

See the updated table below for which panel version to use:

Kit lot	Panel version	Old panel name	New panel name
2502–2506	Immuno 155	proxiome-immuno-155-v2	proxiome-v1-immuno-155-v1.0
2502–2506	Immuno 155 + FMC63	proxiome-immuno-156-FMC63-v2	proxiome-v1-immuno-156-FMC63-v1.0
2507 and above	Immuno 155 v1.1	proxiome-immuno-155-v3	proxiome-v1-immuno-155-v1.1
2507 and above	Immuno 155 v1.1 + FLAG	proxiome-immuno-156-FLAG-v3	proxiome-v1-immuno-156-FLAG-v1.1
2507 and above	Immuno 155 v1.1 + FMC63	proxiome-immuno-156-FMC63-v3	proxiome-v1-immuno-156-FMC63-v1.1

The old panel names no longer work; please specify the new panel name instead.

Added

• Add the option to calculate proximity scores from edgelist using analytical expected join counts.
  PNAPixelDataset.proximity(calculate_from_edgelist=True) is used to compute these scores.

• New implementation of pixelator single-cell-pna graph,
  This version introduces a new workflow, combining a pre-processing step
  using the fast label propagation algorithm, a main step using the Leiden
  algorithm, and a second Leiden refinement pass on the remaining cell
  clusters.

  Finally, this introduces an optional crossing edge filter step using cycle verification.

  This replaces the old graph command, which has been renamed into graph_legacy.

  Instead of parameters --min-component-size-in-refinement and
  --min-component-size-to-prune, this new implementation uses a common
  threshold set by --component-size-min-threshold, or 8000 by default.

• Dependency: pixelgen-pixelator-core (Python bindings for the native graph step).

• Add new optional field archived to panel metadata.

• The parameter --list-panels now lists panels without the archived metadata field.

• Add new option --list-panels-including-archived to list all panels including archived ones.

• Add bundled proxiome-v2 assay design and proxiome-v2-immuno-155-v1.0 panel resources.

• Add support for resolving PNA panels by product name in config lookup.

• Add support for inline panel version specifiers in panel identifiers (for example panel==1.1.0).

Changed

• The previous implementation has been renamed and is available with pixelator single-cell-pna graph_legacy.
• Rename bundled PNA v1 resources to proxiome-v1-* naming for assays and panels. IMPORTANT: the old panel names no longer work. To rerun old data, update relevant scripts to the new panel name(s).
• Remove all panel aliases. Use the correct panel name, or alternatively use a product name with a version specifier to select the panel.
• Panel selection is now stricter when multiple versions exist: ambiguous major/minor requests raise errors and require explicit version disambiguation.
• Panel metadata validation now requires front matter with name and a parseable version.

Parameters

• pixelator single-cell-pna graph

Old parameter	New parameter
	--edge-cycle-verification
--leiden-iterations
--min-component-size-in-refinement
--min-component-size-to-prune

Note

Parameter has been updated if both old and new parameter information is present.
Parameter has been added if just the new parameter information is present.
Parameter has been removed if new parameter information isn't present.

Fixed

• Calculate double-sided p-values instead of single-sided for proximity scores.
• sample calling will now use the pool name in the file name of undetermined
  components to avoid file name collisions in the pipeline.
• Improve the error message when concatenating AnnData objects with incompatible marker (var) schemas.

0.25.0

[0.25.0] - 2026-04-15

Added

• Add sample calling functionality
• Add FLAG and FMC63 v3 panels

Changed

• Change default value for parameter axis of function clr_transformation to be 1.
• Refactor IO classes to handle .pxl files

Fixed

• Fix logging for log1p_transformation and clr_transformation to state that the stats correspond to components and not nodes.
• Fix bug in unpacking 4bit packed sequences.
• Fix bug in sample calling that removed the ending of antibodies that ended with -<digit>.

0.24.0

[0.24.0] - 2026-03-16

Added

• Add progress status updates to the log for amplicon and demux steps in case of non-tty runs, handled by LogProgress utility class.
• Update README with proximity network assay citation information.
• The degree distribution of UMIs is now included in the collapse report.
• New logging messages about the amount of shared memory requested and available from the collapse step
• Add DownloadableDatasets helper to download example datasets

Changed

• Use 64-bit unsigned integers for counts in collapse step to support >4.2B reads.
• Remove the warning when setting minimum size manually. It is observed that 8000 is a
  reliable minimum size for components.

Fixed

• Ensure that additional adata columns are not removed in the denoise step.
• Ensure temporary files are cleaned up in the layout step.
• Droped UMI tools as dependency to avoid build issues.
• Filtering was not working consistently across all data modalities of the pixeldataset

0.23.0

[0.23.0] - 2025-12-01

Important changes

To avoid mistakes in choosing panels, the default panel alias proxiome-immuno-155 has been removed.
Users must now explicitly choose a panel version when using Pixelator with PNA data depending on
which kit lot has been used to produce the data. See the table below for which panel version to use:

Kit lot	Panel version	Panel name
2502–2506	Immuno 155	proxiome-immuno-155-v2
2502–2506	Immuno 155 + FMC63	proxiome-immuno-156-FMC63-v2
2507 and above	Immuno 155 v1.1	proxiome-immuno-155-v3
2507 and above	Immuno 155 v1.1 + FLAG	proxiome-immuno-156-FLAG-v3
2507 and above	Immuno 155 v1.1 + FMC63	proxiome-immuno-156-FMC63-v3

Added

• Support for Python 3.13.
• Add a new filter controlled by the --low-complexity flag to pixelator single-cell-pna amplicon.
  This filter removes reads with UMIs with low sequence complexity. The threshold can be controlled
  using the --umi-complexity-threshold parameter. This filter is enabled by default.
• Add a new filter controlled by the --lbs-filter flag pixelator single-cell-pna amplicon.
  This filter removes UMIs where a linker binding site (LBS) sequence is found within a UMI sequence.
  The filtering behavior can be controlled using the --lbs-filter-min-overlap and
  --lbs-filter-error-rate parameters. This filter is enabled by default.
• proxiome-immuno-155-v3 panel added with new barcode sequences for CD49e, CD79a, and ICOS.
• Improve the panel file validation by checking for white-spaces in marker ids.

Changed

• Moved from using poetry to uv for dependency management and packaging.
• Better performance when reading adata from multiple pxl files.

Fixed

• Fix an issue with DuckDB connection initialization that caused configured memory limits for
  pixelator single-cell-pna combine-collapse to be ignored.

0.22.1

[0.22.1] - 2025-10-31

Fixed

• Panel data can now be fetched from the .pxl file in the denoise step
• control is now stored as boolean in the Panel object, instead of yes/no.
• Fix an error in the "Linker binding site 1" region of the pna-2 assay config file