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Updated: Apr 20, 2026
Automated Quantification and Analysis of Cell Counting Procedures Using ImageJ Plugins
Published on: November 17, 2016
NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei
Axel Poulet1, Ignacio Arganda-Carreras1, David Legland2
1UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.
NucleusJ is a user-friendly ImageJ plugin for 3D nuclear morphology and chromatin organization analysis. It quantifies 15 nuclear parameters, aiding researchers in detailed cellular structure characterization.
Area of Science:
- Cell biology
- Bioimaging
- Computational biology
Background:
- Accurate characterization of nuclear morphology and chromatin organization is crucial for understanding cellular functions and disease states.
- Existing tools may lack user-friendliness or comprehensive analysis capabilities for 3D nuclear data.
Purpose of the Study:
- To introduce NucleusJ, a novel ImageJ plugin for the detailed analysis of 3D nuclear morphology and chromatin organization.
- To provide a user-friendly tool for quantifying nuclear shape, size, and intra-nuclear object features.
Main Methods:
- ImageJ plugin development for 3D image stack analysis.
- Nuclear boundary segmentation using Otsu's method and sphericity optimization.
- Chromatin domain segmentation via 3D watershed algorithm and contrast thresholding.
Main Results:
- NucleusJ quantifies 15 parameters, including nuclear shape, size, and intra-nuclear object characteristics.
- The plugin provides detailed positional information of intra-nuclear objects.
- Step-by-step documentation and sample datasets are provided for user training.
Conclusions:
- NucleusJ offers a simple yet powerful solution for researchers studying nuclear structure in 3D.
- The plugin facilitates quantitative analysis of nuclear morphology and chromatin organization, supporting various biological investigations.
