Pixel Spacing and Slice Thickness of my 3D data are different, in other words, grid of x/y axis is different from grid of z axis.
Will ITK filters still work on this type of images?
If not, how to make modifications? Maybe use interpolation to generate isotropic images?
ITK Images have proper support for such anisotropic images. This is controlled by different voxel spacing along Z axis. Read more in description of itk::ImageBase.