denissch/mcmicro-1

Multiple-choice microscopy pipeline

mcmicro: Multiple-choice microscopy pipeline

mcmicro is an end-to-end processing pipeline for multiplexed whole slide imaging and tissue microarrays. 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 a bioRxiv preprint and accompanied by the following resources:

Resource	URL
Code repository	YOU ARE HERE
Instruction manual	http://mcmicro.org/
EMIT dataset	https://www.synapse.org/EMIT
Tonsil images	https://www.synapse.org/MCMICRO_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/exemplar.nf --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.

Funding

This work is supported by the following:

• 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

Contributors