Cimini, Conceptualization, Investigation, Methodology, Project administration, Software, Validation, Writing – review & editing, # 1 Kyle W. 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. 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. Carpenter, Conceptualization, Funding acquisition, Project administration, Resources, Supervision, Writing – original draft, Writing – review & editing 1, * Caicedo, Software, Writing – review & editing, 1 and Anne E.
S2 Fig: Segmentation steps for the analysis of mouse embryo blastocyst nuclei stained with Hoechst. Images are available from the Broad Bioimage Benchmark Collection ( ), as in Fig 2A of the main paper. (A) Original 3D image of blastocyst nuclei prior to analysis. (B) Evaluation of CellProfiler 3.0 performance in comparison to the MorphoLibJ plugin in Fiji software. Both were compared to manually annotated ground truth using CellProfiler’s MeasureImageOverlap module. (C) CellProfiler 3.0 image processing modules used for blastocyst nuclei segmentation.
Cellprofiler fiji macro manual#
(D) Ground truth obtained by manual annotation of each Z-slice using GIMP software.
Cellprofiler fiji macro code#
(E) Image processing done using Fiji’s MorphoLibJ plugin (macro code is presented in S1 Table). Images were obtained using PerkinElmer Ultraview VoX spinning disk microscope with a 63× immersion objective (distance between Z-slices = 0. 5 μ m) and provided by Javier Frias Aldeguer and Nicolas Rivron from Hubrecht Institute, Netherlands. S3 Fig: Segmentation steps for the analysis of mouse trophoblast stem cell nuclei stained with Hoechst. use the same values across all images to standardize them. Do this for all images systematically i.e. FIJI (Image J) by NIH 4 Before importing the files into Image J, they must be adjusted so that the fluorescent layer is as bright as possible. Images are available from the Broad Bioimage Benchmark Collection ( ), as in Fig 2B of the main paper. CellProfiler by The CellProfiler project team is based in the Carpenter Lab at the Broad Institute of Harvard and MIT.
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