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A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.

Project description


python-version MIT DOI conda pypi Tests

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

Pixelator is a software package to process sequencing FASTQ from Molecular Pixelation (MPX) 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.

Pixelgen Technologies

© 2023 - Pixelgen Technologies AB


More information about pixelator is available on the Pixelgen Technologies Software documentation site.


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, even if installed in Windows WSL.

It should only take a few minutes to install pixelator on any modern computer using any of the following methods.

Installation with pip

Our software 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 with conda / mamba

A conda package is available on the bioconda channel and can be installed with conda or mamba.

conda install -c bioconda pixelator


mamba install -c bioconda pixelator

Installation from source

You can also install pixelator from source by cloning the repository.

git clone
cd pixelator
pip install .

Using docker

The pixelator command-line tool can be run with docker images available on the GitHub container registry.

docker pull
docker run pixelator --help

You can also use the containers provided by the biocontainers project on


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.


Contribution are welcome! Please check out the contributing guidelines for more information.


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


Pixelator is licensed under the MIT license.


Pixelator is developed and maintained by the developers at Pixelgen Technologies.

When using pixelator in your research, please cite the following publication:

Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, et al. “Molecular Pixelation: Single Cell Spatial Proteomics by Sequencing.” bioRxiv, June 8, 2023.

Main development happened thanks to:

A huge thank you to all code contributors!

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