Wrong orientation when using the ImageStacks module

I have a set of mouse brain images (Coronal Serial sections). When I load a single image as “Any Data”, the image appears correctly.

However, when I use the ImageStacks module, the R and G views show a thin image and the Y view shows a fuzzy image.

Is there some option that needs to be set for the orientation?

Looks like you are till in Preview mode in ImageStacks. Clicking full resolution should help. Also it looks like your data are not 1x1x1mm, but likely much more thickly sliced in the Z axis, so you can adjust that (ideally to a known value from your experiment). Once you have it loaded you can adjust the orientation using the Transforms module.

Please check the tutorial about setting the image spacing correctly when you are importing data via ImageStacks.