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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.

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