nf-core/mcmicro

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

NextflowGroovyPythonHTMLworkflowpipelinenextflowimage-processingspatialstitchingregistrationsegmentationimage-analysissingle-cellmicroscopyome-tiffnf-coretmabioformatsmultiplexed-imaging
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Introduction Warning: 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/. :::warning Please provide pipeline parameters via the CLI or Nextflow -params-file option....
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