- Home | MCMICRO
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 tutorial
Following this tutorial can verify that MCMICRO is correctly installed and running on your computer by demonstrating the expected inputs and outputs for the exemplar datasets
- Overview - MCMICRO
MCMICRO provides customizable software that processes whole slide microscopy data into cohesive images that can be easily visualized and quantified as single cell data
- Installation - MCMICRO
MCMICRO source code is licensed under MIT License Contents of this site is licensed under Edit this page on GitHub
- Inputs Outputs | MCMICRO
Turn on the tma setting in workflow parameters to have MCMICRO identify and isolate individual cores Each core will be written out into a standalone file in the dearray subdirectory along with the mask specifying where in the original image the core appeared:
- How to use this website | MCMICRO
Overview provides relevant background information related to multiplexed tissue imaging and MCMICRO View a visual guide through the steps of MCMICRO, then download example data to try it yourself!
- Example datasets - MCMICRO
This detailed visual guide walks you through the MCMICRO pipeline steps as it processes exemplar-002 This guide was generated using the Minerva software package
- Options | MCMICRO
MCMICRO allows users to automatically apply SCIMAP’s clustering algorithms to the cell-by-feature table produced by MCQuant The clustering results can be subsequently used for manual assignment of cell states
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