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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 illumination correction, 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, including local machines, job-scheduling clusters and cloud environments like AWS and GCP. The pipeline execution is implemented in Nextflow, a workflow language that facilitates caching of partial results, dynamic restarts, extensive logging and resource usage reports.

The pipeline is described in a bioRxiv preprint and accompanied by the following resources:

Code repository
Instruction manualYOU ARE HERE
EMIT dataset
Tonsil images

Quick start

  1. Install nextflow and Docker. Check with nextflow run hello and docker images to make sure both are functional.
  2. Download exemplar data. E.g., nextflow run labsyspharm/mcmicro/ --name exemplar-001 --path . to download to current directory.
  3. Run mcmicro on the exemplars. E.g., nextflow pull labsyspharm/mcmicro followed by nextflow run labsyspharm/mcmicro --in exemplar-001 to execute in current directory.

On an average workstation, it takes approximately 5-10 minutes to process exemplar-001 from start to finish. Exemplar-002 is substantially larger, and its processing takes 30-40 minutes on an average workstation.


Development of MCMICRO is led by Artem Sokolov and Denis Schapiro at Laboratory of Systems Pharmacology, Harvard Medical School. Full list of Contributors and Code of Conduct are also available in this documentation.


This work is supported by:

  • 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