How to take measurement in 3d viewer using imagej


Hello everyone,

I’m new on using Fiji/ ImageJ, I imported a stack for ankle joint and would like to take measurement in 3D viewer. is that possible in imageJ?
here is a picture of my 3D model and what I’m trying to measure.

Many thanks



Hi @Saud, and welcome!

Can you be more specific as to what properties you want to measure – length, volume, intensity, etc.?

If you want to isolate a subset of the volume, you can edit/crop it in the viewer following the tutorials on this page.

Then with your cropped area you can use measurement tools such as the 3D object counter.

Hope this helps.


Hi @tswayne , thank you for your reply

I’m trying to measure the width of the talus in 3D. I thought using the measurement tools -> Analyze -> Measure would work in 3D viewer but it’s not. Also, the page you provided is out of date :slight_smile: some of the options are not in my menu. I’m using Fiji ‘last version’.

Thank you



Sorry the pages were out of date.

If two points are enough to define the distance you need, then there are a couple of tools that could work.

  • Use the Point List feature in 3D Viewer (see “How to add/remove points” and “How to save a point list to file”). Those features really do work :slight_smile: except the Point List is under the Landmarks menu. Use the Pythagorean Theorem to get the 3D distance between the points.


  • Use the 3D Distance macro tool to mark points on the original stack (not in 3D viewer). To use the tool, save the file as text, then in ImageJ, go to Plugins > Macros > Install… and you’ll get the tool in your toolbar:28 PM


Thank you @tswayne, it works!