Bug #6530
open
Particle picks off center with K3
Added by Scott Stagg over 5 years ago.
Updated almost 5 years ago.
Affected Version:
Appion/Leginon 3.4
Description
I'm having an instance of that old error where particle picks are systematically offset in one direction. I remember we had this issue a couple of years ago, but I thought it was fixed. Does anybody remember how we fixed this?
I don't remember the fix, but K3/K2 has specific problem with binning that need to be considered.
The picking program generally bin the images by 4 to reduce processing time, but K3/K2 image dimension can not be properly divided by 4 in its physical pixel mode. It may impact the location it come out with.
- Related to Bug #2930: zero degree particles are not centered added
- Related to Bug #4904: FindEM produces artifacts when image dimensions have a large prime factor added
Hi Scott, it is in the python created images, the web image viewer, or both.
If it is both and you are using FindEM, then could be related to bug #4904 with weird image dimensions, I have to trim edges and have not done proper testing.
- Related to Bug #5133: picks not centered added
It's both. The particles are off center when I make a stack
I figured it out. The images were being trimmed both for binning and for picking. The picks were located on the trimmed images and applied to the untrimmed image without accounting for the trimmed pixels. It works now. Let me know if it works on your system.
Thanks for the fix. We don't have k3, yet.
FYI, it was probably an issue for the K2 as well, but you were just living with it.
Also available in: Atom
PDF