Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole-Mount Plant Tissue Using NucleusJ

Methods Mol Biol. 2018:1675:615-632. doi: 10.1007/978-1-4939-7318-7_33.


Image analysis is a classical way to study nuclear organization. While nuclear organization used to be investigated by colorimetric or fluorescent labeling of DNA or specific nuclear compartments, new methods in microscopy imaging now enable qualitative and quantitative analyses of chromatin pattern, and nuclear size and shape. Several procedures have been developed to prepare samples in order to collect 3D images for the analysis of spatial chromatin organization, but only few preserve the positional information of the cell within its tissue context. Here, we describe a whole mount tissue preparation procedure coupled to DNA staining using the PicoGreen® intercalating agent suitable for image analysis of the nucleus in living and fixed tissues. 3D Image analysis is then performed using NucleusJ, an open source ImageJ plugin, which allows for quantifying variations in nuclear morphology such as nuclear volume, sphericity, elongation, and flatness as well as in heterochromatin content and position in respect to the nuclear periphery.

Keywords: 3D nuclear morphology; Chromocenters; Heterochromatin; ImageJ; Nucleus; NucleusJ.

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / ultrastructure
  • Cell Nucleus / genetics
  • Cell Nucleus / ultrastructure*
  • Heterochromatin / ultrastructure*
  • Image Processing, Computer-Assisted / methods
  • Imaging, Three-Dimensional / methods


  • Heterochromatin