Pixelator

Documentation | Installation | Usage | Contributing | Contact | License | Credits

Pixelator is a software package to process sequencing FASTQ from Molecular Pixelation (MPX) and Proximity Network (PNA) assays and analyze PXL data.

It provides the pixelator commandline 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

Additional installation instructions

For running some of the MPX related pixelator commands you will need to have fastp installed on you system. For installation instructions, please visit the fastp GitHub repository.

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

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.

However, with MPX data, we recommend running pixelator in specialized hardware with at least 32GB RAM.

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!