{"repo":"nf-core/imcyto","free":true,"listed":false,"github":"https://github.com/nf-core/imcyto","clone":"git clone https://github.com/nf-core/imcyto.git","description":"Image Mass Cytometry analysis pipeline","language":"Python","stars":26,"topics":["nf-core","nextflow","workflow","image-analysis","image-processing","image-segmentation","cytometry","pipeline"],"license":"MIT","category":"media-processing","readme_excerpt":"Introduction nfcore/imcyto is a bioinformatics analysis pipeline used for image segmentation and extraction of single cell expression data. This pipeline was generated for Imaging Mass Cytometry data, however, it is flexible enough to be applicable to other types of imaging data e.g. immunofluorescence/immunohistochemistry data. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. Pipeline summary 1. Split image acquisition output files ( mcd , ome.tiff or txt ) by ROI and convert to individual tiff files for channels with names matching those defined in user-provided metadata.csv file. Full and ilastik stacks will be generated separately for all channels being analysed in single cell expression analysis, and for channels being used to generate the cell mask, respectively (imctools). 2. Apply pre-processing filters to full stack tiff files (CellProfiler). 3. Use selected tiff files in ilastik stack to generate a composite RGB image representative of the plasma membranes and nuclei of all cells (CellProfiler). 4. Use composite cell map to apply pixel classification for membranes, nuclei or background, and save probabilities map as tiff (Ilastik). If CellProfiler modules alone are deemed sufficient to achieve a reliable segmentation mask this step can be bypassed using the --skip ilastik parameter in which ","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/imcyto/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."}