Package inra.ijpb.plugins

Class AnalyzeRegions3D

java.lang.Object
inra.ijpb.plugins.AnalyzeRegions3D
All Implemented Interfaces:
ij.plugin.PlugIn
public class AnalyzeRegions3D
extends java.lang.Object
implements ij.plugin.PlugIn
Plugin for measuring geometric quantities such as volume, surface area, and eventually sphericity index. Volume is obtained by counting the number of voxels. Surface area is computed using discretization of Crofton formula. Sphericity is obtained as the ratio of V^2 by S^3, multiplied by 36*pi. If the input image is calibrated, the spatial resolution is taken into account for computing geometric features.
Author:
David Legland
See Also:
IntrinsicVolumes3D

  • Field Summary

    Fields
    Modifier and Type Field Description
    boolean debug
    When this options is set to true, information messages are displayed on the console, and the number of counts for each direction is included in results table.

  • Constructor Summary

    Constructors
    Constructor Description
    AnalyzeRegions3D()  

  • Method Summary

    Modifier and Type Method Description
    ij.measure.ResultsTable process​(ij.ImagePlus imagePlus)
    Computes features from an ImagePlus object.
    ij.measure.ResultsTable process​(ij.ImageStack image, ij.measure.Calibration calib)
    Computes features from an ImageStack object, specifying the calibration.
    void run​(java.lang.String args)  

    Methods inherited from class java.lang.Object

    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • debug

      public boolean debug
      When this options is set to true, information messages are displayed on the console, and the number of counts for each direction is included in results table.

  • Constructor Details

    • AnalyzeRegions3D

      public AnalyzeRegions3D()

  • Method Details

    • run

      public void run​(java.lang.String args)
      Specified by:
      run in interface ij.plugin.PlugIn

    • process

      public ij.measure.ResultsTable process​(ij.ImagePlus imagePlus)
      Computes features from an ImagePlus object. Spatial resolution is read from image Calibration.
      Parameters:
      imagePlus - the label image to analyze
      Returns:
      the results in a new ResultsTable

    • process

      public ij.measure.ResultsTable process​(ij.ImageStack image, ij.measure.Calibration calib)
      Computes features from an ImageStack object, specifying the calibration.
      Parameters:
      image - the 3D label image to analyze
      calib - the spatial calibration of the image
      Returns:
      the results in a new ResultsTable