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NucleusJ2.0

NucleusJ 2.0 is a new release of NucleusJ, in which image processing is achieved more quickly using a command-line user 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 unmarked nucleoli.

A discrete geometric method was introduced to improve the surface area calculation, a key parameter when studying nuclear morphology, replacing an imageJ default tool by a new one that includes pixel context information.

To increase the number of nuclei considered in a single analysis, a method was introduced to delimit an automatic bounding volume (autocrop) around each nucleus of a 3D wide-field stack containing ten to a hundred nuclei. Each of the collected nuclei can then be segmented through two complementary methods, either based on the Otsu threshold method or on edge-detection through a 3D gift-wrapping method.

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What's new

The gift wrapping algorithm has been replaced by a graham scan algorithm which is more efficient. Thus, the speed of the segmentation is enhanced.

Download and manual user links

Download the latest version: jar

Manual user and examples: wiki

Authors & contact

Axel Poulet

Dubos Tristan

Contact: tristan.duos33@gmail.com

How to cite :

Tristan Dubos, Axel Poulet, Céline Gonthier-Gueret, Guillaume Mougeot, Emmanuel Vanrobays, Yanru Li, Sylvie Tutois, Emilie Pery, Frédéric Chausse, Aline V. Probst, Christophe Tatout & Sophie Desset (2020) Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0, Nucleus, 11:1, 315-329, DOI: 10.1080/19491034.2020.1845012