Pixelator
Documentation | Installation | Usage | Contributing | Contact | License | Credits
Pixelator is a software package to process sequencing FASTQ from Proximity Network Assay (PNA) experiments and analyze PXL data.
It provides the pixelator command-line tool to process FASTQ files and generate PXL files and reports
and can be used as a Python library for further downstream processing.
Documentation
More information about pixelator is available on the Pixelgen Technologies Software documentation site.
Installation
Pixelgen Technologies has developed and tested pixelator extensively in Ubuntu 20.04.6 LTS. However, pixelator should run on computers installed with any recent version of the major Linux distributions.
Pixelator is available on PyPI as pixelgen-pixelator and can be installed with pip. It is recommended to install pixelator in a separate virtual environment.
pip install pixelgen-pixelator
Installation from source
You can also install pixelator from source by cloning the repository.
git clone https://github.com/pixelgentechnologies/pixelator.git
cd pixelator
pip install .
Using docker
The pixelator command-line tool can be run with docker images available on
the Quay container registry.
docker pull quay.io/pixelgen-technologies/pixelator:latest
docker run quay.io/pixelgen-technologies/pixelator:latest pixelator --help
For deprecated MPX workflows, pin an image tag from a release prior to 0.31.0 (for example 0.30.0) instead of latest.
Usage
Our recommendation is to use pixelator via the specific Nextflow pipeline, nf-core/pixelator.
It should take only a few seconds to download the pipeline and approx. 20 min to run the default test dataset in a normal commodity computer.
Contributing
Contribution are welcome! Please check out the contributing guidelines for more information.
Contact
For feature requests or bug reports, please use the GitHub issues. For questions, comments, or suggestions you can use the GitHub discussions.
You can also email the development team at developers@pixelgen.com.
License
Pixelator is licensed under the MIT license.
Credits
Pixelator is developed and maintained by the developers at Pixelgen Technologies.
When using pixelator in your research, please cite the following publication if you are working with Proximity Network Assay data:
Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, et al.. "Single-Cell Protein Interactomes by the Proximity Network Assay". bioRxiv 2025.06.19.660329; doi: https://doi.org/10.1101/2025.06.19.660329
And for Molecular Pixelation data, please cite:
Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, et al. "Molecular pixelation: spatial proteomics of single cells by sequencing." Nature Methods, May 8, 2024. https://doi.org/10.1038/s41592-024-02268-9.
Main development happened thanks to:
- Jose Fernandez Navarro (@jfnavarro)
- Alvaro Martinez Barrio (@ambarrio)
- Johan Dahlberg (@johandahlberg)
- Florian De Temmerman (@fbdtemme)
A huge thank you to all code contributors!
2 maintainers
Metadata
2 maintainers
Release files for pixelgen-pixelator 0.31.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| pixelgen_pixelator-0.31.0.tar.gz | 499.4 kB | With provenance | Details for pixelgen_pixelator-0.31.0.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| pixelgen_pixelator-0.31.0-py3-none-any.whl | Python 3 | none | any | Details for pixelgen_pixelator-0.31.0-py3-none-any.whl |
Total release size: 1.2 MB
Release files / pixelgen_pixelator-0.31.0.tar.gz
| Download URL | pixelgen_pixelator-0.31.0.tar.gz |
|---|---|
| Size | 499.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
850f42656da84fec24e5e90497ccbd7e8b7acbc9f29b48b9d4b31f509771cd9c
|
|
BLAKE2b-256 checksum How to use checksums |
a0fa326756e45d04993a56a7819cb7394453e9f2a2fb59e2bfa3d04565f47c42
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.16
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 29, 2026.
Transparency logRelease files / pixelgen_pixelator-0.31.0-py3-none-any.whl
| Download URL | pixelgen_pixelator-0.31.0-py3-none-any.whl |
|---|---|
| Size | 668.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
b92e1574cc2831b91f80e51b2ad4d291143056a99d2e22f8ce409d875ba2ea60
|
|
BLAKE2b-256 checksum How to use checksums |
26294b11375f04c20e16a312341957677e4ec7de97a5a401d421177ef41779dc
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.16
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 29, 2026.
Transparency logSecurity for pixelgen-pixelator 0.31.0
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
Full provenance
All 2 files in this release have been uploaded with provenance metadata.
Attestation for pixelgen_pixelator-0.31.0.tar.gz
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 29, 2026.
Transparency logA note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
