Link Search Menu Expand Document

Multiple-choice microscopy pipeline

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data. This website is a consolidated source of information for when, why, and how to use MCMICRO.



Images to insights

Multiplexed tissue imaging provides deep insight into the composition, organization, and phenotype of normal and diseased tissues. MCMICRO converts these multiplexed images into single-cell data using state of the art algorithms. Single-cell resolution images provide spatial context of the cellular microenvironment and can be used alongside additional profiling methods like scRNA-Seq to make robust biological conclusions.

Open source pipeline

MCMICRO is an open source, community supported software that uses Docker and workflow software to create pipelines for analyzing microscopy-based images of tissues. MCMICRO processes data sequentially using algorithms (modules) developed in different research groups.

Modular tools for a new field

High-plex tissue imaging is a new interdisciplinary field involving a wide range of imaging technologies, and the best image analysis approach is not always clear. MCMICRO implements a “multiple choice” approach that allows users to select different modules for customized image processing.

Flexible implementation

MCMICRO is implemented in the workflow languages Nextflow and Galaxy. Both implementations can be run locally, on a compute cluster, or on the cloud.

A growing community

Modules are being added to MCMICRO incrementally by a diverse developer community seeded by the NCI Human Tissue Atlas Network. See what modules we are currently using, view our growing community, or get help.

Robust test data

MCMICRO comes with a growing library of imaging data (EMIT data) for testing your test run or for developing new algorithms. There is a lot of unexplored biology in the test data as well!

Technology agnostic

MCMICRO works with any image that meets the BioFormats standard, most commonly OME-TIFF. These images can be acquired using a wide range of technologies- CODEX, CyCIF, mIHC, mxIF, IMC or MIBI.

Evolving best practices

The MCMICRO team is collaborating with the NCI to run hackathons and challenges to identify the best modules and pipelines for specific types of data.

Table of contents