Creating a 3 D image out of a stack of images with ROIs

Hello again,

I’m trying to get a three dimensional image out of ROIs that I created in a stack of images.

I’m sorry since it might be an easy question but I searched here in the Forum and tried a bit on image j but wasn’t very successful to find a guidance. I seem to overlook it somehow.

Would be happy for a hint how to get it, thank you,


@haesleinhuepf, if you hadn’t seen this post.

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Hi @tarantina,

the issue you mention is not very trivial, but also not very hard. I can give you a rough guide:

You should use a tool like the segmentation editor to outline the objects you’re interested in:

Afterwards, you can use the 3D Roi Manager to organise your data.

To get it running in your Fiji installation, just enable the “3D ImageJ Suite” update site like explained here:

From the 3D ROI Manager, you can also call the 3D Viewer for visualisation.