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Tristan Dubos edited this page Oct 6, 2020 · 22 revisions

Table of content

[[TOC]]

Abstract

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.

How to install NucleusJ2.0

You can download NucleusJ2.0 jar . There is 2 ways to use it :

  • Installation and use from fiji/imageJ : download the jar file and install it in fiji/imageJ plugin folder (more details here ).

  • Use Command Line Interface : all NucleusJ2.0 process are available in command line mode. More details for use it and available parameters here.

List of main fonctions available

  • Autoctop : process rely on a simple Otsu threshold method to isolate object from wide-field image, filter can work with specific threshold or connected component. More details method and utilisation here.

  • Nuclei segmentation

  • Chromocenter segmentation

List of additional fonctions

  • Compute parameters after segmentation

  • Generate projection after nuclei filtering

  • Crop from coordinates

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