[0.21.4] - 2025-08-27

Added

Support limited concurrent access to pixelfiles for selected read-only operations

Fixed

Reduce memory usage during layout computation.
Fix support for single-end reads.

- Python
Published by ptajvar 10 months ago

[0.21.3] - 2025-07-04

Fixed

Fix support for long over-lapping reads in paired-end amplicon.

- Python
Published by ptajvar 12 months ago

[0.21.2] - 2025-06-26

Added

We now distribute container images on quay.io.

Fixed

Performance regression in graph causing memory usage to grow by a factor of two.

- Python
Published by johandahlberg 12 months ago

[0.21.1] - 2025-06-24

Fixed

Added missing gzip dependency in docker container

- Python
Published by johandahlberg 12 months ago

[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.

- Python
Published by johandahlberg 12 months ago

[0.20.1] - 2025-04-24

Changed

The source dist no longer includes the tests directory since this is to big to upload to PyPI when including the necessary test data.

- Python
Published by johandahlberg about 1 year ago

[0.20.0] - 2025-04-24

This is a large release that reorganizes Pixelator in a major way. We introduce the new module pixelator.pna, which is used to process and analyze data from the Proximity Network Assay (PNA). As a consequence of this, we have moved what used to be Pixelator into two modules: pixelator.mpx for processing and analyzing Molecular Pixelation (MPX) data, and pixelator.common, which contains functions and classes used by both methods.

As a user, the most noticeable difference is that if you want to read pixel files to work with MPX data, you will now need to use:

Molecular Pixelation data

from pixelator import read_mpx from pixelator import simple_aggregate_mpx

Proximity Network Assay data

from pixelator import read_pna

With the introduction of the Proximity Network Assay, we have revamped the entire data processing pipeline to handle the new data type. We have also introduced a new pixel file format that utilizes DuckDB files to store the data. This allows us to be much more flexible and faster in loading and processing the data compared to the zip-based format we use for MPX data.

Another major workflow change in how Pixelator is used to work with Proximity Network Assay data is that there is no need to explicitly aggregate data. Instead, the read_pna function accepts a list of files and automatically aggregates the data for you, without the need to create a new aggregated PXL file.

For an updated view on how to work with Pixelator, please check out the documentation. There, you will also find updates on the new algorithms used for the Proximity Network Assay, etc.

Added

All functionality for analyzing PNA data.

Changed

The command-line entry point for MPX data has changed from pixelator single-cell to pixelator single-cell-mpx.

For analysis of MPX data, you should now read MPX data like this:

``` from pixelator import read_mpx

pxldataset = readmpx("path/to/pxl") ```

The function dsb_normalize is now a common method for both MPX and PNA data:

from pixelator.common.statistics import dsb_normalize

Fixed

In some cases, local_g would return scrambled results due to inconsistent node ordering. This has now been fixed.

- Python
Published by johandahlberg about 1 year ago

pixelgen-pixelator - v0.19.0

[0.19.0] - 2024-12-10

Changed

Name components using UPI hashes.
Run multiple iterations of multiplet recovery during the graph stage specified using --max-refinement-recursion-depth.
Specify maximum number of edges that can be removed between two sub-components during multiplet recovery using --max-edges-to-split.
Support for MultiGraphs in pmds_layout
Support multiple targets in plot_colocalization_diff_volcano and plot_colocalization_diff_heatmap.
If demultiplexing has a success rate lower than 50% the command will exit with a status of 1. This prevents further pipeline stages to be run on what is probably bad data.
Clarify that --min-size and --max-size in the annotate stage should not be used at the same time as --dynamic-filter.
Setting a lower threshold of 300 edges when --dynamic-filter is used in the annotate stage, components smaller than that will always be filtered. Note that this can still be overridden by setting --min-size explicitly.
Clarify error message when all components are filtered out in the annotate stage.

Added

Add depth column to discarded_edgelist.parquet output of the graph stage that indicates at which refinement iteration the edge is removed.
Add edges_removed_in_multiplet_recovery_first_iteration, edges_removed_in_multiplet_recovery_refinement and fraction_edges_removed_in_refinement to graph report.json.
Add is_potential_doublet and n_edges_to_split_doublet columns to adata.obs.
Add fraction_potential_doublets and n_edges_to_split_potential_doublets to annotate report.json.
Add --max-edges-to-split option to graph to specify the maximum number of edges that can be removed between two sub-components during multiplet recovery.
Add abundance_colocalization_plot function to make scatter plots of selected marker-pairs' abundance.
Add plot_polarity_diff_volcano to make statistical comparison plots of selected component groups.
Add get_differential_polarity to statistically compare polarity scores of selected component groups.

Removed

Remove the components_recovered.csv output from the graph stage.

Fixed

Improved error message when the number of nodes is lower than the number of requested dimensions in pmds_layout.

Full Changelog: https://github.com/PixelgenTechnologies/pixelator/compare/v0.18.3...v0.19.0

- Python
Published by ambarrio over 1 year ago

pixelgen-pixelator - v0.18.3

[0.18.3] - 2024-09-26

Fixed

Improved memory usage when aggregating PXL files with precomputed layouts.

Full Changelog: https://github.com/PixelgenTechnologies/pixelator/compare/v0.18.2...v0.18.3

- Python
Published by ambarrio over 1 year ago

pixelgen-pixelator - v0.17.3

[0.17.3] - 2024-08-29

Fixed

A bug in compute_transition_probabilities when k>1 where the weight matrix was not computed correctly. This bug also affected the results from local_g when k>1 which results in invalid Z scores.

Full Changelog: https://github.com/PixelgenTechnologies/pixelator/compare/v0.17.2...v0.17.3

- Python
Published by ludvigla almost 2 years ago

pixelgen-pixelator - v0.16.3

[0.16.3] - 2024-07-29

Fixed

Pin scipy version to be compatible with triu function used in the 0.16 series

Full Changelog: https://github.com/PixelgenTechnologies/pixelator/compare/v0.16.2...v0.16.3

- Python
Published by ambarrio almost 2 years ago

pixelgen-pixelator - v0.18.2

[0.18.2] - 2024-07-16

Changed

Bump polars to stable 1.x series

Fixed

Fix a qc report crash issue when the layout stage is run in a pipeline due to an unsupported parameter type.

- Python
Published by johandahlberg almost 2 years ago

pixelgen-pixelator - v0.17.2

[0.17.2] - 2024-07-12

Bump umi_tools version requirements
Fix a bug in aggregating files with precomputed layouts, where the lazy-loading of the layouts was not working correctly.

Full Changelog: https://github.com/PixelgenTechnologies/pixelator/compare/v0.17.1...v0.17.2

- Python
Published by fbdtemme almost 2 years ago

pixelgen-pixelator - v0.18.1

[0.18.1] - 2024-07-12

Changed

Bump umi_tools version requirements

- Python
Published by johandahlberg almost 2 years ago

pixelgen-pixelator - v0.18.0

[0.18.0] - 2024-07-11

Added

Add minimum marker count colocalization_min_marker_count parameter to calculate colocalization score.
Add density_scatter_plot function to make two-marker abundance scatter plots with pseudo-density coloring.
Add wpmds option in pmds_layout to compute edge weighted layouts. This is now set as the default layout algorithm.
Add dsb_normalization function for normalization of marker abundance.
Add a Fraction of Outlier Cells metric to the QC report.
Add a Panel Version metadata field to the QC report.
Add support for datasets generated using the human-sc-immunology-spatial-proteomics-2 panel.

Changed

The default value for normalize_counts in local_g is now False instead of True.
The default transformation for the calculation of the colocalization score is now rate-diff instead of log1p.
Rename edge_rank_plot function to molecule_rank_plot.

Fixed

Fix a bug in compute_transition_probabilities when k>1 where the stochastic matrix was not correctly row-normalized.
Fix a bug in local_g when use_weights=False where the adjacency matrix was not correctly expended if k>1.
Fix a bug where a_pixels_per_b_pixel summary statistics where equal to the b_pixels_per_a_pixel statistics.
collapse will return exit code 137 when one of the child processes is killed by the system (e.g. because it is to much memory). This allows e.g. Nextflow to retry the process with more memory automatically.
Hide the Sample Description metadata field in the QC report when no value is available.
Fix an issue where boolean parameters were formatted as integers in the Parameters section of the QC report.
Fix a bug in aggregating files with precomputed layouts, where the lazy-loading of the layouts was not working correctly.

Removed

Remove the Pixel Version metadata field from the QC report.

- Python
Published by ambarrio almost 2 years ago

pixelgen-pixelator - v0.17.1

[0.17.1] - 2024-05-27

Fixed

Poor performance when writing many small layouts to pxl file (~45x speed-up). This should almost only impact test scenarios, since most real components should be large enough for this not to be an issue.

- Python
Published by johandahlberg about 2 years ago

pixelgen-pixelator - v0.17.0

[0.17.0] - 2024-05-23

Added

Add rate_diff_transformation function with rate-diff alias as an alternative option for transforming marker counts before colocalization calculation.
Add local_g function to compute spatial autocorrelation of marker counts per node.
Add compute_transition_probabilities function to compute transition probabilities for k-step random walks for node pairs in a graph.
Add QC plot showing UMIs per UPIA vs Tau.
Add plot functions showing edge rank and cell counts.
Add 2D and 3D graph plot functions.
Add heatmap plot functions showing colocalization and differential colocalization.
Add volcano plot (value difference vs log p-value) function for differential colocalization.
Add a function to calculate the differential colocalization between two conditions.
Performance improvements and reduced bundle size in QC report.
Improved console output in verbose mode.
Improved logging from multiprocessing jobs.
Improved runtime for graph creation.
Added PMDS layout algorithm.
Add --sample_name option to single-cell amplicon to overwrite the name derived from the input filename.
Add --skip-input-checks option to single-cell amplicon to make input filename checks warnings instead of errors.
PixelDataset instances are now written to disk without creating intermediate files on-disk.
A nice string representation for the Graph class, to let you know how many nodes and edges there are in the current graph object instance.
Metric to collect molecules (edges) in cells with outlier distributions of antibodies (aggregates).
Provide typed interfaces for all per-stage report files using pydantic.
Centralize pixelator intermediate file lookup and access.
Add a precomputed_layouts property to PixelDataset to allow for loading precomputed layouts.
Add pixelator single-cell layout stage to pixelator, which allows users to compute layouts for a PXL file that can then be used to visualize the graph in 2D or 3D downstream.
Add minimum marker count polarization_min_marker_count parameter to calculate Polarity Score.
Add "log1p" as an alternative for PolarizationNormalizationTypes.
Add convert_indices_to_integers option when creating graphs.
Add a feature flag module to aid in the development of new features.

Changed

Change name and description of Avg. Reads per Cell and Avg. Reads Usable per Cell in QC report.
The output name of the .pxl file from the annotate step is now *.annotated.dataset.pxl.
The output name of the .pxl file from the analysis step is now *.analysis.dataset.pxl.
The term edges in metrics and adata is now replaced with molecules.
Renaming of variables in per-stage JSON reports.
Changed name of TCRb to TCRVb5 antibody in human-immunology-panel file and bumped to version 0.5.0.
Renaming of component metrics in adata.
Use MPX graph compatible permutation strategy when calculating Moran's I related statistics.
Marker filtering is now done after count transformation in polarization score calculation.
Use the input read count at the annotate stage for the fraction_antibody_reads_in_outliers metric denominator instead of the total raw input reads.
Use common analysis engine to orchestrate running different "per component" analyses, like polarization and colocalization analysis (yielding a roughly 3x speed-up over the previous approach).
The default transformation for the calculation of the polarity score is now log1p instead of clr.

Fixed

Fix a bug in how discarded UMIs are calculated and reported.
Fix deflated counts in the edgelist after collapse.
Fix a bug where an r1 or r2 in the directory part of a read file would break file name sanity checks.
Fix a bug where the wrong r1 or r2 in the filename would be removed when multiple matches are present.
Logging would cause deadlocks in multiprocessing scenarios, this has been resolved by switching to a server/client-based logging system.
Fix a bug in the amplicon stage where read suffixes were not correctly recognized.
Ensure deterministic results from pmds_layout (given a set seed).
Fix an issue with the fraction_antibody_reads_usable_per_cell metric where the denominator read count was not correctly averaged with the cell count.

Removed

Remove multi-sample processing from all single-cell subcommands.
Remove --input1_pattern and --input2_pattern from single-cell amplicon command.
Self-correlations, e.g. CD8 vs CD8 are no longer part of the colocalization results, as these values will always be undefined.
Remove umi_unique_count and upi_unique_count from edgelist.
Remove umi and median_umi_degree from component metrics.
Remove normalized_rel and denoised from obsm in anndata.
Remove the denoise function.
Remove cell type selector in QC report for UMAP colored by molecule count plots.
Remove clr as a transformation option in pixelator analysis.

- Python
Published by johandahlberg about 2 years ago

pixelgen-pixelator - v0.16.2

[0.16.2] - 2024-03-19

Fixed

Uninitialized value for --polarization-n-permutations

- Python
Published by ptajvar about 2 years ago

pixelgen-pixelator - v0.16.1

[0.16.1] - 2024-01-12

Fixed

Bug in README shield formatting

- Python
Published by johandahlberg over 2 years ago

pixelgen-pixelator - v0.16.0

[0.16.0] - 2024-01-12

This release introduces two major change in pixelator: 1) the Graph backend has been switched from using igraph to using networkx 2) the license has been changed from GLP2.0 to MIT

Added

Experimental 3D heatmap plotting feature.
Optional caching of layouts to speed up computations in some scenarios.
experimental mark that can be added to functions that are not yet production ready.
The underlying graph instance e.g. a networkx Graph instance is exposed as a property called raw from the pixelator Graph class.
Monte Carlo permutations supported when calculating Moran's I (morans_z_sim) in polarization_scores.

Changed

The default (and only) graph backend in pixelator is now based on networkx.
mean_reads and median_reads in adata.obs to mean_reads_per_molecule and median_reads_per_molecule respectively.
Drop support for python 3.8 and 3.9.
Change output format of collapse from csv to parquet.
Change input and output format of graph from csv to parquet.
Change input format of annotate from csv to parquet.
Rename the report to "qc report"
Add a Reads per Molecule frequency figure to the sequencing section of the qc report.
Remove placeholder warning of missing data for not yet implemented features.
Change "Median antibody molecules per cell" to "Average antibody molecules per cell" in the qc report.
Refactoring of the graph backend implementations module.
Speeding up the amplicon step by roughly 3x.

Fixed

Nicer error messages when there are no components valid for computing colocalization.
A bunch of warnings.

Removed

graph no longer outputs the raw edge list.
igraph has been dropped as a graph backend for pixelator.

- Python
Published by johandahlberg over 2 years ago

pixelgen-pixelator - v0.15.2

[0.15.2] - 2023-10-23

Fixed

Fixed broken pixeldataset aggregation for more than two samples.
Fixed a bug in graph generation caused by accidentally writing the index to the parquet file. For backwards compatiblity, if there is an column named index in the edgelist, this will be removed and the user will get a warning indicating that this has happened.

- Python
Published by johandahlberg over 2 years ago

pixelgen-pixelator - v0.15.1

[0.15.1] - 2023-10-18

Fixed

Fixed a bug in filtering pixeldataset causing it to return the wrong types.
Fixed a bug in graph layout generation due to incorrect data frame concatenation.

- Python
Published by fbdtemme over 2 years ago

pixelgen-pixelator - v0.15.0

[0.15.0] - 2023-10-16

Added

Add support for Python 3.11.
Add early enablement work for a networkx backend for the graph stage.

Fixed

Fix report color axis in report figures not updating when selecting markers or cell types.
Remove placeholder links in report tooltips.
Fix a bug where aggregating data did not add the correct sample, and unique component columns.

- Python
Published by fbdtemme over 2 years ago

pixelgen-pixelator - v0.14.0

[0.14.0] - 2023-10-05

Added

Lazy option for edge list loading (pixeldataset.edgelist_lazy), which returns a polars LazyFrame that can be used to operate on the edge list without reading all of it into memory.
Option (ignore_edgelists) to skip the edge lists when aggregating files. This defaults to False.

Changed

Types on the edge list in memory will utilize the pandas category type for string, and uint16 for numeric values to lower the memory consumption when working with the edge list
Remove --pbs1 and --pbs2 commandline arguments to pixelator single-cell adapterqc.
Restructure report figures.
Improve metric names and tooltips in the report.
Synchronize zoom level between the scatter plots in cell annotations section of the report.
Add report placeholder for missing cell annotation data
Add Fraction of discarded UMIs and Avg. Reads per Molecule metrics to the report.

Fixed

Fix an issue where pixelator --version would return 0.0.0 when installing in editable mode.

- Python
Published by fbdtemme over 2 years ago

pixelgen-pixelator - v0.13.1

[0.13.1] - 2023-09-15

Changed

Unpin igraph dependency to allow for newer versions of igraph to be used.
Cleanup README and point to the external documentation site.
Change PyPi package name to pixelgen-pixelator.

Fixed

Fix an issue where --keep-workdirs option for pytest was not available when running pytest without restricting the testdir to tests/integration.
Fix an issue where pixelator --version would return 0.0.0.

- Python
Published by fbdtemme over 2 years ago

pixelgen-pixelator - v0.13.0

[0.13.0] - 2023-09-13

First public release of pixelator

- Python
Published by fbdtemme almost 3 years ago

Recent Releases of pixelgen-pixelator

pixelgen-pixelator - 0.21.4

[0.21.4] - 2025-08-27

Added

Fixed

pixelgen-pixelator - v0.21.3

[0.21.3] - 2025-07-04

Fixed

pixelgen-pixelator - v0.21.2

[0.21.2] - 2025-06-26

Added

Fixed

pixelgen-pixelator - v0.21.1

[0.21.1] - 2025-06-24

Fixed

pixelgen-pixelator - v0.21.0

[0.21.0] - 2025-06-24

Added

Changed

Fixed

pixelgen-pixelator - v0.20.1

[0.20.1] - 2025-04-24

Changed

pixelgen-pixelator - v0.20.0

[0.20.0] - 2025-04-24

Added

Changed

Fixed

pixelgen-pixelator - v0.19.0

[0.19.0] - 2024-12-10

Changed

Added

Removed

Fixed

pixelgen-pixelator - v0.18.3

[0.18.3] - 2024-09-26

Fixed

pixelgen-pixelator - v0.17.3

[0.17.3] - 2024-08-29

Fixed

pixelgen-pixelator - v0.16.3

[0.16.3] - 2024-07-29

Fixed

pixelgen-pixelator - v0.18.2

[0.18.2] - 2024-07-16

Changed

Fixed

pixelgen-pixelator - v0.17.2

[0.17.2] - 2024-07-12

pixelgen-pixelator - v0.18.1

[0.18.1] - 2024-07-12

Changed

pixelgen-pixelator - v0.18.0

[0.18.0] - 2024-07-11

Added

Changed

Fixed

Removed

pixelgen-pixelator - v0.17.1

[0.17.1] - 2024-05-27

Fixed

pixelgen-pixelator - v0.17.0

[0.17.0] - 2024-05-23

Added

Changed

Fixed

Removed

pixelgen-pixelator - v0.16.2

[0.16.2] - 2024-03-19

Fixed

pixelgen-pixelator - v0.16.1

[0.16.1] - 2024-01-12

Fixed

pixelgen-pixelator - v0.16.0

[0.16.0] - 2024-01-12

Added

Changed

Fixed

Removed

pixelgen-pixelator - v0.15.2