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) Based on project statistics from the GitHub repository for the PyPI package CellProfiler, we found that it has been starred 747 times. As such, we scored CellProfiler popularity level to be Small. Using the Worm Toolbox for image analysis of C. The PyPI package CellProfiler receives a total of 555 downloads a week. Identifying and measuring cells: Cytoplasm-nucleus translocation assay ( relevant example pipeline)Ĭalculating and applying illumination correction for images ( relevant example pipeline) Identifying, measuring, and classifying yeast colonies ( relevant example pipeline) Using the Input modules in CellProfiler 2.1: 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. Our introduction to automated image analysis principles and practicalities is published as an educational article at PLoS. Here, we describe how to adapt CellProfiler to analyze cross sections of xylem tissue and use it to gather a variety of information on traits such as cell size, shape, and number. 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. CellProfiler is a free, open source program that allows researchers to automate image analysis and collect large amounts of phenotypic data relatively easily. ImageJ and CellProfiler have long been leading open-source platforms in the field of bioimage analysis. ![]() Visit our YouTube playlist for video tutorials on CellProfiler, CellProfiler Analyst, segmentation strategies, how to construct pipelines, and much more. For the analysis of data described in this paper, we used the latest version (4.2.1) of CellProfiler downloaded from the official CellProfiler website (accessed on 11 October 2021) and installed it on a laptop computer (Intel ® Core i7 4500 U CPU 1.80 GHz 2.40 GHz, 8.
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