Resampling an image stack to desired resolution


I have an image stack as a tifffile which was acquired through light sheet microscopy. The pixel spacing is 1.5x1.5x1.5. I don’t have the affine matrix or the origin of the image stack. I wanted to resample this image to 10x10x10 mm resolution. I was wondering how it is done for the Allen Brain data right now. I tried using ANTs but it crashes as the size of the stack is 10 Gb. I have done it right now using rescale in FiJi but somehow I am not satisfied with this hack. I was wondering if someone could help me do this in a more principled way or tell me what the best practice for this kind of operation is. Also is it possible to get the affine matrix or the origin from images acquired through light sheet microscopy

Hi @anorak,

We have collaborators that can routinely do this operation in ANTs for lightsheet data in the sizes that you mentioned. Have you tried posting to the ANTs forum regarding the crashing issues?

If you are going with the Fiji approach, they recommend checking out Fiji macro and Miji and checking in with those user groups.

Ah ok Thanks a lot