Fundamental flaw on particle locations

Hi Cryosparc community

I was trying to transfer particle locations from cryosparc to relion and realized something is off with particle locations in cryosparc.

The particle coordinates on long axis of a K3 image is reported from 0 to 4092 and short axis is reported from 0 to 5760. I am not even sure how the particle extraction can work properly with this behaviour. Either, there is something fundamentally wrong here or I am making a bizarre mistake. Please let me know if you encountered this problem.

I imported motion corrected mrc micro-graphs to cryosparc. I am using v2.14.2. I initially picked particles with topaz and then manually picked particles to confirm this behavior.

To clarify, I manually picked particles close to edge along the long axis of the micrograph, X coordinate was constant and the Y coordinate was increasing from 0 upto 4092. I picked particles along the short axis and the Y coordinate was increasing from 0 to 5760 while the X coordinate was constant.

Hi @alburse,

Presuming you are using @DanielAsarnow’s great pyem tools for conversion?
Please check out this post for some discussion about x/y conventions.