(E) Image processing done using Fiji’s MorphoLibJ plugin (macro code is presented in S1 Table).
CELLPROFILER PROPERTIES FILE MANUAL
(D) Ground truth obtained by manual annotation of each Z-slice using GIMP software. (C) CellProfiler 3.0 image processing modules used for blastocyst nuclei segmentation. 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. 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.
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