Full frame or Patch Motion correction - Defect file incorporation

Hello!

I was wondering if there is a way to incorporate a Defect File while performing Full frame or Patch Motion Correction to account for the defects in the camera? (similar to what motioncor2 does)

Regards,
Kavita

Hi @Kavita,
We don’t currently support external defect files, but full-frame and patch motion both attempt to find defect pixels automatically (i.e. hot pixels). Are you seeing a case where this is insufficient? If possible, it would be great if you can share with us a handful of example movies so we can either add a defect file support or improve our autodetection of defects.
If it is possible to share, please contact us via email at feedback@structura.bio

Hi @apunjani,

Thank you for getting back to me.

The Patch motion correction seems to have one a great job and the final 3D does not seem to be affected by the defective pixels. But the corrected micrographs (Non-doseweighted aligned micrograph) do show 2 vertical stripes (corresponding to the defective rows of pixels).

We would be happy to share movies (how many do you need?).

Regards,
Kavita

Hi @Kavita,
We’ve emailed you to provide upload instructions. Just a handful of movies (5-10) will be enough.

Hi @apunjani,

Have sent over the data!

Kavita

Hi @Kavita,

Thanks! We’re taking a look and will get back to you!

- Suhail

Hi, I have a similar case, the motion correction tools of cryosparc fail to correct for the dead pixels. I then use motioncorr in cryosparc, but when I then run the output in the patch CTF tool, the output is really weird. It looks better when I use gctf from cryosparc. If possible, I would prefer to use the full frame motion from cryosparc. Any advice ? Thanks

@marino-j would you be able to share data for this issue also? It would help us to have more examples. We’ll email to provide upload instructions

@apunjani I have also collected data with defect pixels. When I run patch motion correction I get this result:
image

The defect pixel line goes through the micrographs where the 2nd and 3rd lowest patches are. It is quite visible to me that the motion has not been corrected in this area.

Would you like to get some of my micrographs as well?

@Valtteri_Jarvinen definitely if you can share your data that would be very helpful!
I will email you to provide upload credentials.
Thanks!

Hi - I can add, that the data my data recorded on the same scope/camera. @apunjani, I uploaded last year some files, did you have any time to look at those ? The solution could surely help Valtterli too. As for Valtterli, what I did back then to get rid of the defect pixel line, is simply to use motioncorr2 either from cryosparc or from relion, as seems to be the only way to input the defect file. Keep me posted.

Thanks !