inra.ijpb.plugins

Class AnalyzeRegions3D

java.lang.Object

inra.ijpb.plugins.AnalyzeRegions3D

All Implemented Interfaces:

ij.plugin.PlugIn

public class AnalyzeRegions3D
extends 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 and 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 and Description
AnalyzeRegions3D()

Method Summary

Modifier and Type	Method and 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(String args)

Methods inherited from class java.lang.Object

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

Field Detail

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 Detail

AnalyzeRegions3D

public AnalyzeRegions3D()

Method Detail

run

public void run(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