Output from the patch motion correction

Hi all,

I have a quick question. I am trying to analyze the *rigid_traj.npy files from the patch motion correction, but the units of the numbers in the array is not clear. I believe it should be pixel or angstrom, but which one is correct? Thank you!

Hi @eon,

The units of the trajectories are in pixels, in terms of the dimensions of the raw movie data. So a trajectory with 1.0 pixel motion corresponds to 1.0 * psize where psize is the pixel size of the input movie data, before any Fourier-cropping.
This pixel size is also recorded in the .cs file that is outputted in patch motion, the field is rigid_motion/psize_A (pixel size in units of Å per pix).

Thank you for the fast response!