Manage automatically the image intensity dynamic

before segmentation, or CC detection, a 3D Gaussian Blur is done with also an increase of the contrast

index problem corrected

Merge pull request #4 from ChariereFiedler/javadoc

Add Javadoc support in Pom.XML

Correction of bug

coorection of some nug and comment
Have to use morpholib 1.2.2
and the imagescience.jar available here
then you need also jama.jar

Tested By Tristan on fiji and imageJ, evrything is working

Correction of segmentation problem (out bound index)

Correction added the 04/12/18,

Correction of index error and dection version problem which involed nucleusJ error

Index bounds error similar to the previous in the version 1.0.2

To use nucleusJ you need to dowload the two depencies available here plus jama.jar (See the documentation: http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start).

Imagescience.jar version problem:
(Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 46MB of 5991MB (<1%)
java.lang.NoClassDefFoundError: imagescience/utility/ImageScience
at gred.nucleus.myGradient.MyEdges.run(MyEdges.java:47)
at gred.nucleus.myGradient.MyGradient.run(MyGradient.java:74)
at gred.nucleus.core.ChromocentersEnhancement.applyEnhanceChromocenters(ChromocentersEnhancement.java:32)
at gred.nucleus.plugins.ChromocenterSegmentationBatchPlugin_.run(ChromocenterSegmentationBatchPlugin_.java:65)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)

Morphlib error:

Creation of image of the CC without no image, that is due at nucleusJ which is working with the version of MorpholibJ_-1.2.2 or anterior.

NucleusJ

Correct error in the NucleusSegmentation, which involved the early stop of the process.
Test realised on FIJI and imageJ:

java.lang.IndexOutOfBoundsException
at ij.ImageStack.getVoxel(ImageStack.java:373)
at gred.nucleus.core.NucleusSegmentation.isVoxelThresholded(NucleusSegmentation.java:218)
at gred.nucleus.core.NucleusSegmentation.applySegmentation(NucleusSegmentation.java:118)
at gred.nucleus.core.NucleusSegmentation.run(NucleusSegmentation.java:53)
at gred.nucleus.plugins.NucleusSegmentationAndAnalysisPlugin_.run(NucleusSegmentationAndAnalysisPlugin_.java:63)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)

First release of NucleusJ

v1.0.1

release