Hi there,
I would like to use particles extracted from CryoSPARC with other softwares. However, I cannot find the convention used for the image grid of single particles.
For example, it seems Relion and XMIPP use the same convention for the centre of the image:
https://www.scripps.edu/milligan/docs/xmipp/Conventions.html
as well as eman2 (except the origin is bottom left):
https://blake.bcm.edu/emanwiki/EMAN2/TransformInPython
What about CryoSPARC ? I could not find that information on the website.
Thank you very much !
Hi @x_gabdu! Welcome to the forum!
CryoSPARC treats the bottom left pixel as [0,0]. We believe that this is the convention followed by all cryoEM reconstruction packages — you may want to double-check the other conventions. This issue is somewhat confused by the fact that the coordinate (0, 0) in physical space is often treated differently from pixel position [0,0] in the images.
If you want to move data between CryoSPARC and other refinement packages, you can most likely use Daniel Asarnow’s pyem library to do this, which would save you the heartache of considering the various pose and pixel conventions of the programs.
I hope that is helpful!