NucleusJ

NucleusJ is an ImageJ plugin that characterizes nuclear morphology and chromatin organization in 3D. It uses the Otsu segmentation method and optimization of nuclear sphericity to delimit the nuclear boundary, and a 3D watershed algorithm and thresholding to segment chromatin domains. NucleusJ provides 15 quantifiable parameters including nuclear shape and size, intra-nuclear objects, and their position within the nucleus. It also includes a step-by-step documentation for self-training and data sets of nuclei with different nuclear organization.

Topic

Nucleic acid structure analysis;Cell biology;Imaging

Detail

  • Operation: Image analysis

  • Software interface: Graphical user interface

  • Language: Java

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: Auvergne and Oxford Brookes universities, the French National Research Agency, Infrastructure TEFOR/ANR-11-INBS-0014 by the Region Auvergne.

  • Input: -

  • Output: -

  • Contact: pouletaxel@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei.
  • Poulet A, et al. NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei. NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei. 2015; 31:1144-6. doi: 10.1093/bioinformatics/btu774
  • https://doi.org/10.1093/bioinformatics/btu774
  • PMID: 25416749
  • PMC: -

Download and documentation

    Currently not available or not maintained.

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