ROI 3D manager not running

Usage & Issues
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#1

Hi, I would like to work on the 3D manager to process my Z stack pictures and do nuclear segmentation and evaluate 3D FISH signals distance and relocation in my nuclei.
I installed all the plugins from ImageJ3Dsuite and others (TANGO, Bio formats, LOCI…) on my macbook and I am Not able to run the 3D manager when I launch it. I get a message in the console “not starting RoiManager3D”, just before: ‘imagescience not installed, please install from http://…’ but cannot Install required featureJ_.jar and imagescience.jar packages, also getting an error message.

Thanks for your help

#2

Hi @MarieCecileGaillard,

If you want to use 3D Manager you need to download imagescience.jar and copy it into your ImageJ or Fiji plugins directory, you can find this package here. If you use Fiji simply activate the ImageScience update site.

Hope this helps and do not hesitate to contact me if you need help using the 3D Suite.

Best,

Thomas

#3

thank you @ThomasBoudier, I was lacking the imagescience update so it works now I can access the consol of the 3D manager. I will actually need some help to process my pictures in the 3D suite. I am doing acquisition of 3D FISH on mES cells mostly (that grow in colonies). I succeed to keep them as much single cells as I can to do measurements and I generate about 100 stacks for each. I would like to apply segmentation of nuclei, and distances measurments between probe/nuclear periphery or probe/nuclei center to see if there is movment of my signals from these compartments (heterochromatin). For now I am stuck to process the pile of Z stacks, I am loading my file correctly (.nd with every Channels and Z stacks) and I can see it. From that then if I press ‘add image’ or ‘3D segmentation’ in the 3D manager It is Processing for a while (my cursor is loading) but nothing happened then. Would it be a capacity Problem to process the all thing in the plugin or should I do things in a different order, work on separated channel first …?

Thanks for your help,
Best,
Marie-Cecile

#4

Hi @MarieCecileGaillard,

3D Manager is used to analyse already segmented data, you need first to segment your nuclei. For 3D segmentation of nuclei you can try 3D Object Counter, or my experimental 3D Nuclei segmentation. Once you have labelled data, you can add them to 3D Manager. You can upload an image if you need help for segmentation.

Best,

Thomas