![]() We also post guided exercises as part of our educational outreach effort. Simple nuclei identification tutorial ( sample data) (courtesy of the German BioImaging network) Performing a colocalization assay ( relevant example pipeline) Using the Worm Toolbox for image analysis of C. pixels across all color planes come from the same measurement and could affect each other (e.g. When produced through Imaging Mass Cytometry, these images are 'intrinsically' aligned, e.g. Identifying and measuring cells: Cytoplasm-nucleus translocation assay ( relevant example pipeline)Ĭalculating and applying illumination correction for images ( relevant example pipeline) This repository contains CellProfiler plugins developed to facilitate working with highly multiplexed images (>40 channels). Identifying, measuring, and classifying yeast colonies ( relevant example pipeline) These efforts not only expand the functionality of CellProfiler and CellProfiler Analyst but also leverage the strengths of other packages. Using the Input modules in CellProfiler 2.1: Software for analyzing CellProfiler-produced data Software Partnerships CellProfiler has partnered with academic and commercial groups to create a variety of software interfaces. Using CellProfiler for Quantitative Image Analysis The NIH has published a introductory chapter of “best practices” for image-based high-content screening (in which CellProfiler is mentioned) as part of the Assay Guidance Manual, and our group has published a more advanced follow-up chapter on image analysis methods. ![]() Once you have results you need to decide on a method of organization. If you have a large dataset and you want to get it analyzed sometime this century you need to split your analysis, run, and then gather the results. Our introduction to automated image analysis principles and practicalities is published as an educational article at PLoS. Keep track of dependencies of CellProfiler Analyses first run an illumination correction and then your analysis. Technical descriptions of CellProfiler and CellProfiler Analyst software can be found in our papers while more written tutorials can be found on the CellProfiler GitHub page. Visit our YouTube playlist for video tutorials on CellProfiler, CellProfiler Analyst, segmentation strategies, how to construct pipelines, and much more.
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