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
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).