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Tristan Dubos edited this page Mar 3, 2021 · 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 :

  • Use NucleusJ2 with an graphical interface through fiji/imageJ : download the jar file and install it in fiji/imageJ plugin folder (more details here).

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

Before starting

Most of of functionalities of NucleusJ2 are computationally expensive (depending on your image input of course) . We recommend to have at least 8Go of RAM. If you want to use NucleusJ2 as fiji/imageJ plugin , you must increase default memory value (more information here)

List of main fonctions available

  • Autoctop : process that relies on a simple Otsu threshold method to isolate object from wide-field image, filters with specific threshold or connected component.More details on the method and use here.

  • Nucleus segmentation : method to segment nucleus isolated in a single image. We use a Otsu threshold and a Gift-wrapping method to segment nuclei, more details here

  • Chromocenter segmentation

List of additional fonctions

  • Compute parameters after segmentation

  • Generate projection after nuclei filtering

  • Crop from coordinates

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