NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei | Zendy

Axel Poulet | Zendy; Ignacio ArgandaCarreras | Zendy; David Legland | Zendy; Aline V. Probst | Zendy; Philippe Andrey | Zendy; Christophe Tatout | Zendy

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NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei

Author(s) -

Axel Poulet,

Ignacio ArgandaCarreras,

David Legland,

Aline V. Probst,

Philippe Andrey,

Christophe Tatout

Publication year - 2014

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btu774

Subject(s) - plug in , computer science , thresholding , nucleus , chromatin , artificial intelligence , segmentation , sphericity , computer graphics (images) , pattern recognition (psychology) , physics , image (mathematics) , biology , operating system , microbiology and biotechnology , dna , genetics , astronomy

NucleusJ is a simple and user-friendly ImageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D. Starting from image stacks, the nuclear boundary is delimited by combining the Otsu segmentation method with optimization of nuclear sphericity. Chromatin domains are segmented by partitioning the nucleus using a 3D watershed algorithm and by thresholding a contrast measure over the resulting regions. As output, NucleusJ quantifies 15 parameters including shape and size of nuclei as well as intra-nuclear objects and their position within the nucleus. A step-by-step documentation is available for self-training, together with data sets of nuclei with different nuclear organization.

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