3D ImageJ Suite GUI Error

@ThomasBoudier

I think I found an error. When I try to open the GUI of the 3D Manager (Menu ‘3D Manager’)
the following error occurs at least on Windows (class not found in the classpath)

grafik

Tested with ImageJ and Bio7

Installation files from:

http://imagejdocu.tudor.lu/plugin/stacks/3d_ij_suite/start

Hi @Bio7,

Usually this problem occurs when ImageScience is not installed.

Best,

Thomas

@ThomasBoudier The imagescience library is installed. Interestingly the 3D Manager options can be opened and some other actions work, too (e.g. 3D Draw Shape doesn’t work).

Hi @Bio7,

I am unable to reproduce the problem, is there something in the Log window like “checking installation …” , maybe it is related to the Java 3D libraries, is 3D viewer working ?

Best,

Thomas

Hello @ThomasBoudier The 3D viewer is not installed. Is the installation mandatory?

Log Window (Debug Mode):

actionPerformed: time=1557296975194, java.awt.event.ActionEvent[ACTION_PERFORMED,cmd=3D Manager,when=1557296975193,modifiers=] on menuitem0
runPlugIn: mcib_plugins.tools.RoiManager3D_2
runUserPlugIn: mcib_plugins.tools.RoiManager3D_2, arg=
runUserPlugIn: rerunning mcib_plugins.tools.RoiManager3D_2
runUserPlugIn: tools.RoiManager3D_2, arg=
GUI.getMaxWindowBounds: java.awt.Rectangle[x=0,y=0,width=1920,height=1160]

Hi @Bio7,

Yes 3DManager requires 3DViewer for visualisation, so interestingly 3D Draw Shape also use 3D Viewer for rendering, this is why it is not working. Actually only the libraries are required, namely org.scijava:j3dcore:1.6.0-scijava-2 . Hope this helps.

Best,

Thomas

Hello @ThomasBoudier It seems that the org.scijava:j3dcore:1.6.0-scijava-2 is not shipped with the deprecated 3D Viewer for ImageJ.

So one have to install the libray from the ImageJ2 resources?

Hi @Bio7,

Yes ImageJ uses an older version of 3DViewer with older libraries, you can either use the libraries shipped with Fiji or use my packaged version here .

Best,

Thomas

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Hello @ThomasBoudier Now it works. Sorry, I think I did not read the instructions thoroughly here:

http://imagejdocu.tudor.lu/plugin/stacks/3d_ij_suite/start

to install the adapted version of the 3D Viewer.

Thanks for your support and keep up that great work!

@ThomasBoudier Just one additional question.

I’m always searching for free example data for teaching.

Do you also have image stack examples available to, e.g., measure particles and distances in 3d?

Hi @Bio7,

I am quite a big fan of nuclei labelled datasets, because you can get many questions asked, for instance you can have a look to the sample data provided with TANGO (go to the Import Images section). I also like 4D datasets, and you can find interesting data in the cell tracking challenge.

Hope this helps,

Thomas

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@ThomasBoudier thanks for the links.