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Imaging Mass Cytometry (IMC) file type support for napari

Project description

napari-imc

napari hub PyPI License Python Version Issues Pull requests

Imaging Mass Cytometry (IMC) file type support for napari

Load panoramas and multi-channel acquisitions co-registered within the machine's coordinate system from Fluidigm TXT/MCD files

Installation

You can install napari-imc via pip:

pip install napari-imc

Alternatively, you can install napari-imc via conda:

conda install -c conda-forge napari-imc

For example, to install napari and napari-imc in a fresh conda environment using pip:

conda create -n napari-imc python=3.9
conda activate napari-imc
pip install "napari[all]" napari-imc

Usage

Simply open your Fluidigm TXT/MCD file using napari.

Authors

Created and maintained by Jonas Windhager jonas.windhager@uzh.ch

Citation

Please cite the following paper when using napari-imc in your work:

Windhager J, Bodenmiller B, Eling N (2021). An end-to-end workflow for multiplexed image processing and analysis. bioRxiv. doi: https://doi.org/10.1101/2021.11.12.468357.

@article{Windhager2021,
  author = {Windhager, Jonas and Bodenmiller, Bernd and Eling, Nils},
  title = {An end-to-end workflow for multiplexed image processing and analysis},
  year = {2021},
  doi = {10.1101/2021.11.12.468357},
  URL = {https://www.biorxiv.org/content/early/2021/11/13/2021.11.12.468357},
  journal = {bioRxiv}
}

Contributing

Contributing

Changelog

Changelog

License

MIT

Project details


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