Gray Scale Attribute Filtering 3D not working

[ClemenceKress]

Hello,

I used Gray Scale Attribute Filtering on 2D image without problem in Fiji (everything updated). I'd like to do the same on 3D images now. But when I try to use Gray Scale Attribute Filtering 3D on a stack, I get the following message:

(Fiji Is Just) ImageJ 2.3.0/1.53f51; Java 1.8.0_202 [64-bit]; Mac OS X 10.16; 44MB of 8004MB (<1%)

java.lang.RuntimeException: Unknown connectivity: 4 at inra.ijpb.morphology.attrfilt.SizeOpening3DQueue.process(SizeOpening3DQueue.java:99) at inra.ijpb.morphology.AttributeFiltering.volumeOpening(AttributeFiltering.java:131) at inra.ijpb.plugins.GrayscaleAttributeFiltering3D.run(GrayscaleAttributeFiltering3D.java:202) at ij.IJ.runUserPlugIn(IJ.java:241) at ij.IJ.runPlugIn(IJ.java:204) at ij.Executer.runCommand(Executer.java:150) at ij.Executer.run(Executer.java:68) at java.lang.Thread.run(Thread.java:748)

I get the same results if I change the connectivity value. Could you help me? Thank you

[dlegland]

Hello,

it looks like a copy-paste error when converting algorithms from 2D to 3D... thanks for reporting, we will check soon!

David

[dlegland]

Well, after checking I realize the bug was alreadyu fixed in August (https://github.com/ijpb/MorphoLibJ/commit/55e7080a321b90dae1a916c3288f367c9909f60a). Therefore, correct version will be available with next release!

[ClemenceKress]

Thank you for the fery fast answer and the good news. And when will the next release be? I can surely use other tools, but if it is very soon I'd better wait.

[dlegland]

There is no official date for the next "big" release; we are currently working on several changes, so a new release could be available "soon"... In the meanwhile, I have released a bug-fix release; you can download it here: https://github.com/ijpb/MorphoLibJ/releases/tag/v1.4.3.1

(simply download the jar, and use it as replacement of previous MorphoLibJ jar in the ."../Fiji.app/plugins" directory)

[ClemenceKress]

Thank you, indeed it works now. Your plugin is great. the distance transform watershed is very efficient for the segmentation of nuclei of various shape and intensity within tissue sections. And the possibilities for label edition are very handy: with merging and manual correction of shapes I manage to obtain a correct segmentation for all nuclei, which is quite remarkable. I also appreciate a lot the documentation about the plugin, it is very clear to understand what the tools do. This is really not the case with some other plugins (I'm currently struggling with other ones for 3D analysis).

[dlegland]

Thank you for your very positive feedback! We are glad the library is useful and can be easily adopted by people. And yes, makng the documentation takes a lot of time, but is absolutely crucial for users!