Issues with scaling information added to .tiff volume- tried ImageStacks and saving as .nrrd?

alsig
Sun, 08 Feb 2026 00:27:54 +0000
Support

Hi everyone,

I am having a issue when trying to import/save TIFF data in a way that lets me add the scaling information. I have a single file ImageJ hyperstack .tiff that has my entire volume, with X-Y scale of 0.001282 microns/pixel and a Z-step size of 0.000641 microns. When I initially loaded it using add data, it opens without any issues, and I can easily scroll through all the slices as expected.

I tried to edit the volume to include the correct spacing/unit conversions, which in my case is (XYZ) like this in the volumes module:

Although that looked fine initially, when I saved the volume from there as a .nrrd, as I saw recommended here to preserve the 3D volume information, and opened the new .nrrd file, I completely lost the ability to see or scroll through the slices, and only had a single slice view. B I tried to import the data using the SlicerMorph ImageStacks extension like this instead, but ended up with a very strange looking volume that did not show up in the viewing planes:

Does anyone have any ideas on how to fix this, or what I am doing wrong? Any advice is greatly appreciated!

11 posts - 3 participants