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Cellprofiler save movie not working6/12/2023 Both were compared to manually annotated ground truth using CellProfiler’s MeasureImageOverlap module. (B) Evaluation of CellProfiler 3.0 performance in comparison to the MorphoLibJ plugin in Fiji software. (A) Original 3D image of blastocyst nuclei prior to analysis. Images are available from the Broad Bioimage Benchmark Collection ( ), as in Fig 2A of the main paper. S2 Fig: Segmentation steps for the analysis of mouse embryo blastocyst nuclei stained with Hoechst. Carpenter, Conceptualization, Funding acquisition, Project administration, Resources, Supervision, Writing – original draft, Writing – review & editing 1, * Caicedo, Software, Writing – review & editing, 1 and Anne E. Rafelski, Conceptualization, Methodology, Project administration, Resources, Supervision, Writing – review & editing, 4 Derek Thirstrup, Data curation, Methodology, Software, Validation, Writing – review & editing, 4 Winfried Wiegraebe, Conceptualization, Methodology, Resources, Supervision, 4 Shantanu Singh, Resources, Software, Writing – review & editing, 1 Tim Becker, Investigation, Software, Visualization, Writing – review & editing, 1 Juan C. Karhohs, Investigation, Methodology, Software, # 1 Minh Doan, Methodology, Software, Writing – original draft, Writing – review & editing, 1 Liya Ding, Data curation, Methodology, Software, Validation, Writing – review & editing, 4 Susanne M. Cimini, Conceptualization, Investigation, Methodology, Project administration, Software, Validation, Writing – review & editing, # 1 Kyle W. We also post guided exercises as part of our educational outreach effort.Claire McQuin, Conceptualization, Formal analysis, Software, Writing – original draft, Writing – review & editing, # 1 Allen Goodman, Conceptualization, Investigation, Software, # 1 Vasiliy Chernyshev, Data curation, Investigation, Methodology, Software, Validation, Visualization, Writing – review & editing, # 2, 3 Lee Kamentsky, Conceptualization, Software, # 1 Beth A. 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. 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. 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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