https://github.com/pixelgentechnologies/pixelator
A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.
https://github.com/pixelgentechnologies/pixelator
molecular-pixelation pixelgen-technologies protein proteomics proximity-network single-cell single-cell-omics spatial
Last synced: about 1 month ago
JSON representation
A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.
- Host: GitHub
- URL: https://github.com/pixelgentechnologies/pixelator
- Owner: PixelgenTechnologies
- License: mit
- Created: 2023-09-13T13:28:14.000Z (almost 3 years ago)
- Default Branch: dev
- Last Pushed: 2026-05-26T14:59:34.000Z (about 1 month ago)
- Last Synced: 2026-05-26T16:34:40.961Z (about 1 month ago)
- Topics: molecular-pixelation, pixelgen-technologies, protein, proteomics, proximity-network, single-cell, single-cell-omics, spatial
- Language: Python
- Homepage: https://pixelgen.com
- Size: 83.2 MB
- Stars: 20
- Watchers: 4
- Forks: 4
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Citation: CITATIONS.md
Awesome Lists containing this project
README
# Pixelator
[](https://opensource.org/licenses/MIT)
[](https://doi.org/10.1038/s41592-024-02268-9)
[](https://bioconda.github.io/recipes/pixelator/README.html#package-pixelator)
[](https://pypi.org/project/pixelgen-pixelator/)
[](https://quay.io/repository/pixelgen-technologies/pixelator)
[](https://github.com/PixelgenTechnologies/pixelator/actions/workflows/tests.yml)
[**Documentation**](#documentation) |
[**Installation**](#installation) |
[**Usage**](#usage) |
[**Contributing**](#contributing) |
[**Contact**](#contact) |
[**License**](#license) |
[**Credits**](#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.
© 2023 - Pixelgen Technologies AB
## Documentation
More information about pixelator is available on the [Pixelgen Technologies Software documentation site](https://software.pixelgen.com/).
## 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.
```shell
pip install pixelgen-pixelator
```
### Additional installation instructions
For runnning 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](https://github.com/OpenGene/fastp).
### Installation from source
You can also install pixelator from source by cloning the repository.
```shell
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](https://quay.io/repository/pixelgen-technologies/pixelator).
```shell
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](https://github.com/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](./CONTRIBUTING.md) for more information.
## Contact
For feature requests or bug reports, please use the GitHub [issues](https://github.com/PixelgenTechnologies/pixelator/issues).
For questions, comments, or suggestions you can use the GitHub [discussions](https://github.com/PixelgenTechnologies/pixelator/discussions).
You can also email the development team at [developers@pixelgen.com](mailto:developers@pixelgen.com).
## License
Pixelator is licensed under the [MIT](./LICENSE) license.
## Credits
Pixelator is developed and maintained by the [developers](https://github.com/PixelgenTechnologies) at [Pixelgen Technologies](https://pixelgen.com).
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](https://github.com/jfnavarro))
- Alvaro Martinez Barrio ([@ambarrio](https://github.com/ambarrio))
- Johan Dahlberg ([@johandahlberg](https://github.com/johandahlberg))
- Florian De Temmerman ([@fbdtemme](https://github.com/fbdtemme))
A huge thank you to all [code contributors](https://github.com/PixelgenTechnologies/pixelator/graphs/contributors)!