{"repo":"nf-core/mcmicro","free":true,"listed":false,"github":"https://github.com/nf-core/mcmicro","clone":"git clone https://github.com/nf-core/mcmicro.git","description":"An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.","language":"Nextflow","stars":35,"topics":["nextflow","nf-core","pipeline","workflow","microscopy","multiplexed-imaging","spatial","tma","bioformats","ome-tiff"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction [!WARNING] We are currently in the process of porting the original MCMICRO to nf-core. This pipeline is therefore in active development. nf-core/mcmicro is a nextflow pipeline for processing highly-multiplexed imaging data, as produced by technologies such as Cycif, MIBI, CODEX, SeqIF among others. If you want to run the original MCMICRO pipeline outside of nf-core, please see . The nf-core/mcmicro pipeline is an end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data. It takes samplesheet and markersheet files as input and perfoms registration, segmentation and quantification. Multiple segmentation modules are available and can be run in parallel. The pipeline can also optionally perform background and shading correction, background subtraction, and supports tissue microarrays. It returns a pre-segmentation image file, a segmentation mask image, and a cell x feature array spreadsheet. The MC in MCMICRO stands for 'Multiple Choice' and that refers to the fact that there will be multiple module options available for many steps in the pipeline. The currently supported options are provided in parentheses for required steps. 1. Registration (Ashlar) 2. Segmentation (Cellpose, Mesmer) 3. Quantification (MCQuant) Usage [!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. First, prepare ","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/mcmicro/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}