Create full image out of µCT-scans


I have a question and would be grateful for your help.
I have µCt scans of Osteons, which are provided in “sliced form”, so if you imagine a osteon as a regular cylinder, I have about 100 slices of osteon-images.

I’d like to have one image per osteon, facing the front of the cylinder, to make judgements about their height to width diameter and also check the quality of their harvesian canals.

Do you know how this would be possible using bonej?

Thanks a lot!


Basically, you would like to inspect your 3D osteon images?
I am not damiliar with BoneJ, but here is how I would do it:
First, you can stack the images together with Import/Image sequence. Then, save the 3D image as TIF, so you can open it later as a single file. You may want to set the spatial resolution at this point with Analyze/Set scale.
You can visualize your volume with 3D viewer.
To make qualitative measurements, angles for example, try Image/Stacks/Orthogonal views
If you need to rotate or crop your specimen, you can use TransformJ.
Tip: Use the search field at the bottom of the Fiji bar to find the commands.

Hope that helps,


Hello again!

Thank you for your response, that was actually exactly what I was looking for.


Now I have this. The only thing that I would be interested now is to “look inside” of the osteon, from this perspective, into the middle, to actually see the Harvesian canal. Is that possible as well?

Sorry for having to ask again, I’m just very new with Fiji/BoneJ.

Thank you!

Hello cheesybread,

I am not sure I understand. Actually, you can use the sliders and the yellow lines to sweep the 3D image in any plane. If you want to look “inside”, you can just zoom. Or did I missed something?


Hi @cheesybread,

In the 3D Viewer you can try the “Orthogonal View” and move the orthogonal slices accordingly


you can give ClearVolume a trial. There you can cut using the box sliders, which enables you to look inside the 3D structure displayed.


You use the normal ►Image►Stacks►Orthogonal Views to do thin in the actual stack.


Hello, Thank you for your helpful replies!

Sorry about not expressing my issue properly, this isn’t easy since english is not my native tongue.
Nevertheless, I solved the issue

I took the orthogonal view-image, and used the “Reslice” command, which created a stack of images for me from the frontal view.

Thank you all for being so helpful! :slight_smile:

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