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. 2020 Dec;11(1):315-329.
doi: 10.1080/19491034.2020.1845012.

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

Tristan Dubos  1 , Axel Poulet  2 , Céline Gonthier-Gueret  3 , Guillaume Mougeot  1   4 , Emmanuel Vanrobays  1 , Yanru Li  5 , Sylvie Tutois  1 , Emilie Pery  6 , Frédéric Chausse  6 , Aline V Probst  1 , Christophe Tatout  1 , Sophie Desset  1
Affiliations

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

Tristan Dubos et al. Nucleus. 2020 Dec.

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.

Keywords: 3D DNA FISH; Three-dimensional microscopy imaging; image analysis; nuclear organization; plant nucleus.

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Conflict of interest statement

No potential conflicts of interest were disclosed.

Figures

Figure 1.
Figure 1.
Application of NucleusJ 2.0 autocrop method on a wide-field stack
Figure 2.
Figure 2.
Evaluation of a 3D gift-wrapping method of segmentation
Figure 3.
Figure 3.
Evaluation of a new method of Surface Area calculation implemented into NucleusJ 2.0
Figure 4.
Figure 4.
NucleusJ2.0 analysis of the k4c1c4 mutant with 1altered nuclear morphology and chromatin organization
Figure 5.
Figure 5.
Analysis of aspect and position of 180pb and 5S rDNA repeats revealed by 3D-DNA FISH using NucleusJ 2.0
See this image and copyright information in PMC

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