# Pixelator
[](https://opensource.org/licenses/MIT)
[](https://www.biorxiv.org/content/10.1101/2023.06.05.543770v1)
[](https://bioconda.github.io/recipes/pixelator/README.html#package-pixelator)
[](https://pypi.org/project/pixelgen-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) 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.
<p align="center">
<img src="https://www.pixelgen.com/wp-content/uploads/2022/12/share-image-pixelgen.png" height=200
alt="Pixelgen Technologies" />
</p>
<div align="center">© 2023 - Pixelgen Technologies AB</div>
## 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, 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.
```shell
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.
```shell
conda install -c bioconda pixelator
```
or
```shell
mamba install -c bioconda pixelator
```
### 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 [GitHub container registry](https://github.com/PixelgenTechnologies/pixelator/pkgs/container/pixelator).
```shell
docker pull ghcr.io/pixelgentechnologies/pixelator:latest
docker run ghcr.io/pixelgentechnologies/pixelator:latest pixelator --help
```
You can also use the containers provided by the biocontainers project on [quay.io](https://quay.io/repository/biocontainers/pixelator).
## 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:
> 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. https://doi.org/10.1101/2023.06.05.543770.
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)!
A non-exhaustive list of contributors follows:
- Filip Karlsson ([@fika-pixelgen](https://github.com/fika-pixelgen))
- Max Karlsson ([@maxkarlsson](https://github.com/maxkarlsson))
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"description": "# Pixelator\n\n\n\n[](https://opensource.org/licenses/MIT)\n[](https://www.biorxiv.org/content/10.1101/2023.06.05.543770v1)\n[](https://bioconda.github.io/recipes/pixelator/README.html#package-pixelator)\n[](https://pypi.org/project/pixelgen-pixelator/)\n[](https://github.com/PixelgenTechnologies/pixelator/actions/workflows/tests.yml)\n\n[**Documentation**](#documentation) |\n[**Installation**](#installation) |\n[**Usage**](#usage) |\n[**Contributing**](#contributing) |\n[**Contact**](#contact) |\n[**License**](#license) |\n[**Credits**](#credits)\n\n\nPixelator is a software package to process sequencing FASTQ from Molecular Pixelation (MPX) assays\nand analyze PXL data.\n\nIt provides the `pixelator` commandline tool to process FASTQ files and generate PXL files and reports\nand can be used as a python library for further downstream processing.\n\n\n<p align=\"center\">\n <img src=\"https://www.pixelgen.com/wp-content/uploads/2022/12/share-image-pixelgen.png\" height=200\n alt=\"Pixelgen Technologies\" />\n</p>\n<div align=\"center\">\u00a9 2023 - Pixelgen Technologies AB</div>\n\n## Documentation\n\nMore information about pixelator is available on the [Pixelgen Technologies Software documentation site](https://software.pixelgen.com/).\n\n## Installation\n\nPixelgen 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.\n\nIt should only take a few minutes to install pixelator on any modern computer using any of the following methods.\n\n### Installation with pip\n\nOur software pixelator is available on PyPi as `pixelgen-pixelator` and can be installed with pip.\nIt is recommended to install pixelator in a separate virtual environment.\n\n```shell\npip install pixelgen-pixelator\n```\n\n### Installation with conda / mamba\n\nA conda package is available on the bioconda channel and can be installed with conda or mamba.\n\n```shell\nconda install -c bioconda pixelator\n```\nor\n```shell\nmamba install -c bioconda pixelator\n```\n\n### Installation from source\n\nYou can also install pixelator from source by cloning the repository.\n\n```shell\ngit clone https://github.com/pixelgentechnologies/pixelator.git\ncd pixelator\npip install .\n```\n\n### Using docker\n\nThe `pixelator` command-line tool can be run with docker images available on\nthe [GitHub container registry](https://github.com/PixelgenTechnologies/pixelator/pkgs/container/pixelator).\n\n```shell\ndocker pull ghcr.io/pixelgentechnologies/pixelator:latest\ndocker run ghcr.io/pixelgentechnologies/pixelator:latest pixelator --help\n```\n\nYou can also use the containers provided by the biocontainers project on [quay.io](https://quay.io/repository/biocontainers/pixelator).\n\n## Usage\n\nOur recommendation is to use pixelator via the specific Nextflow pipeline, [nf-core/pixelator](https://github.com/nf-core/pixelator).\n\nIt 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.\n\nHowever, with MPX data, we recommend running pixelator in specialized hardware with at least 32GB RAM.\n\n## Contributing\n\nContribution are welcome!\nPlease check out the [contributing guidelines](./CONTRIBUTING.md) for more information.\n\n## Contact\n\nFor feature requests or bug reports, please use the GitHub [issues](https://github.com/PixelgenTechnologies/pixelator/issues).\nFor questions, comments, or suggestions you can use the GitHub [discussions](https://github.com/PixelgenTechnologies/pixelator/discussions).\n\nYou can also email the development team at [developers@pixelgen.com](mailto:developers@pixelgen.com).\n\n## License\n\nPixelator is licensed under the [MIT](./LICENSE) license.\n\n## Credits\n\nPixelator is developed and maintained by the [developers](https://github.com/PixelgenTechnologies) at [Pixelgen Technologies](https://pixelgen.com).\n\nWhen using pixelator in your research, please cite the following publication:\n\n> Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, _et al._ \u201cMolecular Pixelation: Single Cell Spatial Proteomics by Sequencing.\u201d bioRxiv, June 8, 2023. https://doi.org/10.1101/2023.06.05.543770.\n\n\nMain development happened thanks to:\n\n- Jose Fernandez Navarro ([@jfnavarro](https://github.com/jfnavarro))\n- Alvaro Martinez Barrio ([@ambarrio](https://github.com/ambarrio))\n- Johan Dahlberg ([@johandahlberg](https://github.com/johandahlberg))\n- Florian De Temmerman ([@fbdtemme](https://github.com/fbdtemme))\n\nA huge thank you to all [code contributors](https://github.com/PixelgenTechnologies/pixelator/graphs/contributors)!\n\nA non-exhaustive list of contributors follows:\n\n- Filip Karlsson ([@fika-pixelgen](https://github.com/fika-pixelgen))\n- Max Karlsson ([@maxkarlsson](https://github.com/maxkarlsson))\n\n",
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