Full frame or Patch Motion correction - Defect file incorporation

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#1

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


#2

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


#3

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


#4

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


#5

Hi @apunjani,

Have sent over the data!

Kavita


#6

Hi @Kavita,

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

- Suhail


#7

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