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3D Analysis

Various plugins for analysis of 3D images and objects.


Thomas Boudier


A plugin for 3D Radial Distribution of voxel values inside a sphere is available, select first a position with the point tool. If you compute the EVF (Eroded Volume Fraction = normalised Euclidean Distance Transform) you can use EVF Distribution to compute information in growing layers of equal volumes.

You can compute co-localisation between labelled objects in two images using the MultiColoc plugin.

3D segmentation and labelling algorithms are available in 3D Segmentation.

A plugin to remove objects on borders of the image (X, Y and Z) is available, and could be used before analysis.

The following plugins work on 3D images of labelled objects (the value of voxel is the numbering of object as in count masks) :

  • 3D Geometrical measurements (volume, surface, …) for each labelled object.
  • 3D Centroid, to compute centroids of labelled objects.
  • 3D Intensity measurements (mean, integrated density, …) in a opened image for each labelled object.
  • 3D Shape measurements (compactness, elongation, …) for each labelled object.
  • 3D Mesh Measurements after triangulation (see 3D Viewer for surface mesh computation).
  • 3D fitting by an ellipsoid and main direction computation (details here).
  • 3D Radial Distance Area Ratio (RDAR)
  • 3D Density, to compute density of dots, based on closest distance analysis (details here).


For details go to the 3D ImageJ Suite.


When using the 3D Analysis plugins for publication, please refer to :

J. Ollion, J. Cochennec, F. Loll, C. Escudé, T. Boudier. (2013) TANGO: A Generic Tool for High-throughput 3D Image Analysis for Studying Nuclear Organization. Bioinformatics 2013 Jul 15;29(14):1840-1. doi


GPL distribution (see license). Sources for plugins are available freely. Sources for core are available on request.

plugin/analysis/3d_analysis/start.txt · Last modified: 2019/08/30 05:25 by tboudier

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