some investigation this morning solved my problem:
the order of the coordinates is wrong, which becomes relevant when micrograph dimensions are not symmetric.
giving micrograph_blob/shape : [X Y]
post-conversion correction can be made by: (coordx/shape X)*shape Y and (coordy/shape Y)*shape X
this will lead to the centered particles.
it would be great if you would change the conversion function in pyem to obsolete this “fix” @DanielAsarnow
I am wondering that nobody was suffering from this before…