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 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 |
- Install nextflow and Docker. Check with
nextflow run helloanddocker imagesto make sure both are functional. - Download exemplar data. E.g.,
nextflow run labsyspharm/mcmicro/exemplar.nf --name exemplar-001 --path .to download to current directory. - Run mcmicro on the exemplars. E.g.,
nextflow pull labsyspharm/mcmicrofollowed bynextflow run labsyspharm/mcmicro --in exemplar-001to execute in current directory.
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