Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0.

Abstract

NucleusJ 1.0, an ImageJ plugin, is a useful tool to analyze nuclear morphology and chromatin organization in plant and animal cells. NucleusJ 2.0 is a new release of NucleusJ, in which image processing is achieved more quickly using a command-lineuser interface. Starting with large collection of 3D nuclei, segmentation can be performed by the previously developed Otsu-modified method or by a new 3D gift-wrapping method, taking better account of nuclear indentations and unstained nucleoli. These two complementary methods are compared for their accuracy by using three types of datasets available to the community at https://www.brookes.ac.uk/indepth/images/ . Finally, NucleusJ 2.0 was evaluated using original plant genetic material by assessing its efficiency on nuclei stained with DNA dyes or after 3D-DNA Fluorescence in situ hybridization. With these improvements, NucleusJ 2.0 permits the generation of large user-curated datasets that will be useful for software benchmarking or to train convolution neural networks.

Code and data availability

The paper's 3D nuclear bio-imaging datasets (7,313 images across six dataset types: digitized spheres, fluorescent microspheres, nuclear morphology, chromatin organization, and DNA FISH) are stored in the public OMERO-FSU repository under accession IDP3006_Dubos-Desset_2020, accessible via the INDEPTH website. The Nuce