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


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;

see docs.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don’t hesitate to get in touch on the Slack #mcmicro channel (you can join with this invite).


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 file.

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.