Leginon

Sorry for missing answering this.

We have been doing beam-image shift targeting up to +/-2.6 um on all Krioses without beam-tilt correction for more than two years as in my paper. That has no overhead involved.

On Cs-corrected scope, we had TFS calibrated beam tilt compensation required to minimize B2 (Coma constant) so that we can do it coma-free.

On non-Cs corrected scopes, we have since summer shifted to add beam-tilt, 2-fold astigmatism, sometimes defocuss correction when image-beam shift is applied. This allows us to go further out, up to +/-7 um.

We use this for 3-5 months now, depending on the scope, and have found that what matters most, the beam tilt correction, is the most stable, and then 2-fold stigmatism. The defocus correction is not stable but it has least impact on data quality. It is certainly worth doing. In the 2-3 Å resolution range structure, we found it comparable with the old setup but gives more images in a given time.

The calibration at the moment uses AutoCTF from TFS to find the correction needed at each beam-image shift. If you don't have the program, you will need to calibrate manually with Beam Tilt Imager and do ctf estimations yourself. The calibration does take 1 to 2 hrs the first time, but is faster if you need to redo later because I apply the previous calibration as the starting value.

This calibration and usage is available in myami-beta branch and myami-3.4 which is ready for release, pending documentation.

Hi Anchi,

We have been starting to work on setting up the beam-image shift and doing the calibration for this, however are unclear exactly how to do this calibration based on the protocol previously posted. Once you get the microscope aligned properly and the parameter settings setup in the Calibrations/Beam Tilt/Toolbar, how do you proceed with the calibration? We are getting error messages that the "Beam tilt has not changed. Will cause calibration failure." Any additional information on running this calibration would be greatly appreciated. FYI we do not have AutoCTF, so we would need to calibrate manually with the Beam Tilt Imager.

Thank you,
Amy

I will need to do some work so that you can do this calibration with Beam Tilt Imager. I just had an idea over the weekend and will implement that quickly in the next few days. Stay tuned.

Hi Anchi,
We want to do this on our Polara and F20. have you made any progress so that we can do the calibration with beam tilt imager? Thanks.

Sorry, forgot to update this thread.

Yes. It is in both beta and 3.4 release. It is not fully automated. You need to adjust coma, stig, and defocus manually, but it has all the tools needed and will set the condition it needs to calibrate at each step for you.

See Lens Aberration Correction Calibration for Beam-Image Shift Targeting and follow the procedure for Using Leginon manual tools to calibrate beam-image shift aberration correction

Hi Anchi,

I followed your new instruction for image-shift coma correction on K3 (no GIF) using manual way, but encountered similar error as Amy Bondy, "Beam tilt has not changed. Will cause calibration failure.", see attachment.
And I noticed image shit was "locked" at "x -10 um, y 0 um" rather than changing to "x -5um, y 0 um" subsequently.
Our other calibration is fine, able to collect data beyond 3A resolution.
Any suggestion on what to check?
Thanks.

Best,
Guang

What is your version ? Have you did a pull of the current head of the version ? There were a few rounds of debug and improvement of interaction 4 months ago.

Can you show me how you know image shift is locked ? For example, show me the settings dialog vs the log window.

On the linux server we're running 3.4, but the Windows instrumentation machines were installed from the current beta as of about 3 weeks ago. Should I just upgrade the server to the most up to date version using git?

While in general I recommend using the same version on the instrument machines and the linux server, you should not have conflict in this case.

I do recommend to a git pull of the 3.4 version on your linux server, though. During investigation of your question, I see that there was a bug fix that should have gone into myami-3.4.

Given that your current 3.4 version should not have the problem Guang described, please check the settings of your Beam Tilt calibration node. Specifically the settings for Image-Shift Coma calibration. It is default like this:

This means it takes 2 measurement in each direction of the beam tilt. Therefore, the beam tilts are (-10 um, 0), (-5 um, 0), (0,0), (5 um, 0), (10 um, 0)

The instruction recommended changing the step to 1 in the initial calibration for speed and ease of calibration. Maybe that was not applied.

Thanks, Anchi. Is there any way I can definitely check that we have leginon 3.4 installed on the server? I have many leginon source directories at this point, and would just like to reality check myself that I actually did install 3.4 on the main processing server.

If it is a git clone, inside the myami directory, just do

git status

It should say

On branch myami-3.4

If it is not a git clone, you can check the content of the file called version.py in the leginon directory of your source,

def getTextVersion():
  return '3.4'

For myami-beta, it would say beta.