An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
We are currently in the process of porting the original MCMICRO to nf-core. This pipeline is therefore in active development.
nf-core/mcmicro is a nextflow pipeline for processing highly-multiplexed imaging data, as produced by technologies such as Cycif, MIBI, CODEX, SeqIF among others.
If you want to run the original MCMICRO pipeline outside of nf-core, please see https://mcmicro.org/.
Please provide pipeline parameters via the CLI or Nextflow
-params-file option. Custom config files including those provided by the
-c Nextflow option can be used to provide any configuration except for parameters;
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
If you use nf-core/mcmicro for your analysis, please cite it using the following article: Schapiro et al. 2022 Nat. Methods
An extensive list of references for the tools used by the pipeline can be found in the
You can cite the
nf-core publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.