napari-imc
October 19, 2023 ยท View on GitHub
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., Zanotelli, V.R.T., Schulz, D. et al. An end-to-end workflow for multiplexed image processing and analysis. Nat Protoc (2023). https://doi.org/10.1038/s41596-023-00881-0
@article{Windhager2023,
author = {Windhager, Jonas and Zanotelli, Vito R.T. and Schulz, Daniel and Meyer, Lasse and Daniel, Michelle and Bodenmiller, Bernd and Eling, Nils},
title = {An end-to-end workflow for multiplexed image processing and analysis},
year = {2023},
doi = {10.1038/s41596-023-00881-0},
URL = {https://www.nature.com/articles/s41596-023-00881-0},
journal = {Nature Protocols}
}