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MCMICRO: Multiple-choice microscopy pipeline

MCMICRO is an end-to-end processing pipeline for multiplexed whole slide imaging and tissue microarrays developed at the HMS Laboratory of Systems Pharmacology. It comprises stitching and registration, segmentation, and single-cell feature extraction. Each step of the pipeline is containerized to enable portable deployment across an array of compute environments.

The pipeline is described in Nature Methods. Please see mcmicro.org for documentation, tutorials, benchmark datasets and more.

Quick start

  1. Install nextflow and Docker. Verify installation with nextflow run hello and docker run hello-world
  2. Download exemplar data: nextflow run labsyspharm/mcmicro/exemplar.nf --name exemplar-001
  3. Run mcmicro on the exemplar: nextflow run labsyspharm/mcmicro --in exemplar-001

Funding

This work is supported by the following:

Contributors