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License: MIT Build Status

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 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/ --name exemplar-001
  3. Run mcmicro on the exemplar: nextflow run labsyspharm/mcmicro --in exemplar-001


This work is supported by the following:

  • NCI grants U54-CA22508U2C-CA233262 and U2C-CA233280
  • NIH grant 1U54CA225088: Systems Pharmacology of Therapeutic and Adverse Responses to Immune Checkpoint and Small Molecule Drugs
  • Ludwig Center at Harvard Medical School and the Ludwig Cancer Research Foundation
  • Denis Schapiro was supported by the University of Zurich BioEntrepreneur-Fellowship (BIOEF-17-001) and a Swiss National Science Foundation Early Postdoc Mobility fellowship (P2ZHP3_181475). He is currently a Damon Runyon Quantitative Biology Fellow
  • NCI grant 1U24CA274494-01: Multi-Consortia Coordinating Center (MC2 Center) for Cancer Biology: Building Interdisciplinary Scientific Communities, Coordinating Impactful Resource Sharing, and Advancing Cancer Research