title: NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei.
abstract: 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.
  
  
  METHODS
  Dataset of nuclei is available at https://www.gred-clermont.fr/media/WorkDirectory.zip. NucleusJ is available at http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.
authors.forename: Axel
authors.initials: A
authors.lastname: Poulet
authors.affiliation: UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.
authors.forename: Ignacio
authors.initials: I
authors.lastname: Arganda-Carreras
authors.affiliation: UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.
authors.forename: David
authors.initials: D
authors.lastname: Legland
authors.affiliation: UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.
authors.forename: Aline V
authors.initials: AV
authors.lastname: Probst
authors.affiliation: UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Andrey
authors.affiliation: UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Tatout
mesh_terms: D000465:Algorithms; D002467:Cell Nucleus / Q000235:genetics*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods; D007399:Interphase / Q000235:genetics*