Large z-spacing, is there a way?

Hi folks, I’ve been trying to work with a stack of histologic images. I would like to do some segmentation and 3d reconstruction (qualitative I guess). I’ve got my images aligned and in a stack, but I cannot set the spacing between slices. My slices are 40um thick, but spaced about 0.8mm apart. Is there a way to deal with this in imageJ? I’ve been poking around, but so far have had no luck. Thanks, David

Hi @dwaugh

To set the spacing between the slices, go to the Image > Properties menu. You have to enter the z stepping of the acquisition device. If I get your message correctly, that would be 0.8mm.


I don’t see that as an option in the in Properties menu. I can set the image or voxel depth there, but not the space between the slices.

I did find an option to set the Z-step in TrakEM2. I will further explore that option, although after setting the z spacing there, the 3d viewer still represented my volume thin like a pancake. I will try doing some segmenting in there, and see if the segmentation will display with correct dimensions.

Any other suggestions welcome!

ImageJ doesn’t distinguish between slice thickness and slice spacing. A pixel (or voxel in 3D) is just a point sample in space, and the voxel depth that is set in Image > Properties… will define the spacing at which the different image planes are displayed in 3D (e.g. in the 3D viewer or the ClearVolume plugins).