Dear guys, I am quite new to ImageJ. Now I got so many micro-CT slices but each of the slices is not at the right horizontal position therefore all of them needs to be change their angle so I can correctly calculate structure parameters like bone volume/tissue volume, trabecular thickness, connectivity and others, by using BoneJ. In short, it there any way to change the horizontal angle of slice (what I mean is also to change the Z-axis which is perpendicular to the slice)? thank you very much in advance!

Hi and welcome to the forum,

you could use the interactive stack rotation plugin for example:

This allows to do manual rotation.

**Plugins > Transform > Interactive Stack Rotation**For non interactive rotations I always use the TransformJ plugin:

https://imagescience.org/meijering/software/transformj/

These are all 3D parameters with no concept of direction, so there is no advantage to rotating the volume. They do assume isotropic pixel spacing, which is usually the case for X-ray microtomography image stacks.

If you need to get images into a common or standard coordinate frame to be able to interpret the fabric tensor (measurement from Anisotropy), which *is* a measure of direction, then rotating the stack may be helpful. You might consider the alternative, which is to calculate the coordinate frame tensor and the fabric tensor on the unrotated (i.e. original image), then rotate the fabric tensor into the coordinate frame tensor with matrix multiplication. The advantage is that you donâ€™t have to create a rotated copy of your image data, which avoids all the interpolation artefacts that will be created.

Another way to do a rotation is using Moments of Inertia in BoneJ, which aligns an image stack according to 3D principal axes. That works well if you have a whole bone such as a mouse tibia in your image stack.