Package inra.ijpb.plugins

Class Watershed3DPlugin

java.lang.Object
inra.ijpb.plugins.Watershed3DPlugin
All Implemented Interfaces:
ij.plugin.PlugIn
public class Watershed3DPlugin
extends java.lang.Object
implements ij.plugin.PlugIn
A plugin to perform watershed on a 3D image using flooding simulations, as described by Soille, Pierre, and Luc M. Vincent. "Determining watersheds in digital pictures via flooding simulations." Lausanne-DL tentative. International Society for Optics and Photonics, 1990.
Author:
Ignacio Arganda-Carreras

  • Field Summary

    Fields
    Modifier and Type Field Description
    static double hMax
    the maximum value for dynamic
    static double hMin
    the minimum value for dynamic
    static boolean use26neighbors
    flag to use 26-connectivity

  • Constructor Summary

    Constructors
    Constructor Description
    Watershed3DPlugin()  

  • Method Summary

    Modifier and Type Method Description
    ij.ImagePlus process​(ij.ImagePlus input, ij.ImagePlus mask, int connectivity, double hMin, double hMax)
    Apply 3D watershed to a 2D or 3D image (it does work for 2D images too).
    void run​(java.lang.String arg)
    Plugin run method, to be called from ImageJ.

    Methods inherited from class java.lang.Object

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

  • Field Details

    • use26neighbors

      public static boolean use26neighbors
      flag to use 26-connectivity

    • hMin

      public static double hMin
      the minimum value for dynamic

    • hMax

      public static double hMax
      the maximum value for dynamic

  • Constructor Details

    • Watershed3DPlugin

      public Watershed3DPlugin()

  • Method Details

    • process

      public ij.ImagePlus process​(ij.ImagePlus input, ij.ImagePlus mask, int connectivity, double hMin, double hMax)
      Apply 3D watershed to a 2D or 3D image (it does work for 2D images too).
      Parameters:
      input - the 2D or 3D image (in principle a "gradient" image)
      mask - binary mask to restrict region of interest
      connectivity - 6 or 26 voxel connectivity
      hMin - minimum grayscale level height
      hMax - maximum grayscale level height
      Returns:
      labeled catchment basins image

    • run

      public void run​(java.lang.String arg)
      Plugin run method, to be called from ImageJ.
      Specified by:
      run in interface ij.plugin.PlugIn