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

<!-- TODO nf-core: Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the major pipeline sections and the types of output it produces. You're giving an overview to someone new to nf-core here, in 15-20 seconds. For an example, see --> <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core workflows use the "tube map" design for that. See for examples. --> <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline --> <!-- ## Usage :::note If you are new to Nextflow and nf-core, please refer to [this page]( on how to set-up Nextflow. Make sure to [test your setup]( with `-profile test` before running the workflow on actual data. ::: <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets. Explain what rows and columns represent. For instance (please edit as appropriate): First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: ```csv sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz ``` Each row represents a fastq file (single-end) or a pair of fastq files (paired end). --> <!-- Now, you can run the pipeline using: --> <!-- TODO nf-core: update the following command to include all required parameters for a minimal example --> <!-- ```bash nextflow run nf-core/mcmicro \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR> ``` -->

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.

<!-- For more details and further functionality, please refer to the [usage documentation]( and the [parameter documentation]( --> <!-- ## Pipeline output To see the results of an example test run with a full size dataset refer to the [results]( tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation]( --> <!-- ## Credits nf-core/mcmicro was originally written by TBD. We thank the following people for their extensive assistance in the development of this pipeline: --> <!-- TODO nf-core: If applicable, make list of people who have also contributed -->

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).


<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. --> <!-- If you use nf-core/mcmicro for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX]( --> <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->

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.