Leginon

Hi, Long,

What you set as Focus setting is correct. Leginon put the screen down during the melting. If you want to be sure, try it out with a non-burning-hazard preset such as fa by set Melt Preset to it and a larger than zero Melt Time. During that time, watch or listen for the sound of screen coming down and back up.

Hello Anchi,

Thank you for your reply. I will test the focus settings with fa at first.

And for the K2 calibration, I remember that there is a beam shift calibration:

http://emg.nysbc.org/projects/leginon/wiki/Beam_Shift_matrix_calibration

Since this calibration needs highly focused beam on the camera, I think that this might not be very good for the K2 camera. So maybe I should skip this beam shift calibration, is that correct?

Cheers,
Long

You caught a good point. I will add a warning in the instruction.

Hi Anchi,
I have two questions regarding Beam shift calibration:
We have an Orius camera at the same plane as the K2 Summit. I understand that it is not advised to do this calibration on the K2. Is is possible/desirable to perform Beam shift calibration using the Orius camera?
The second question is whether the calibration is useful at all in MSI operation. Is is possible to introduce a step that checks for beam centering in MSI-T2 for example? Would the system be able to switch between cameras?

The problem that I am trying to preempt is in the the beam boundary getting into the image for cases where image/beam shift are used to center the exposure area. I understand that this should be done when aligning the scope, but sometimes it is slightly off.

Thanks

Mario

Mario,

It is indeed possible. Whether it is desirable or not, that is harder to say. Being on the sample plan as K2 and half the size, you will have to condense the beam further when you make adjustment of beam shift. With perfect alignment like on Krios in your case, the center is maintained, then you can add a preset using Orius, and do beam shift alignment during data collection.

MSI-T, MSI-Edger, MSI-Raster and their 2 client variants have a node called "Fix Beam" that is meant for automated beam shift alignment. We don't use it on tecnai series microscope since the algorithm is quite a simple one. It just moves the beam at the chosen preset in x at fix intervals and the pick the one that gives the highest mean intensity in the image it takes. As you can see it is good if the beam is way off but not not effective when you only want fine adjustment to be away from Fresnel fringes.

You are welcome to try it though. In its settings you need to give it how often you want it to check and adjust it, the preset used to do so which can be on the Orius or K2 since we don't change the beam intensity when doing this, and the presets that you want the adjusted beam tilt to apply to.

See Gatan_K2_Instruments_cfg for the correct z plane assignment for adding Orius. While it is physically on the same plane as K2, it is not capable of pushing K2 out so we have to set it on a different z plane from software point of view.

Hi Anchi,
Thanks for the detailed response!
I have something to add regarding the Orius. At least in our configuration it is necessary to specify dimensions for Leginon to recognize the presence of the camera.

[camera2]
class: dmsem.GatanOrius
zplane: 29
width: 2096
height: 2088

BTW, we have another 4k CCD pre-GIF in our Krios, I have therefore decided to number the planes as follows

50 Gatan BM Ultrascan
30 Gatan K2 Summit in all the variants
29 Gatan Orius

The three cameras are in two separate files of course, the post gif in the gatan computer and the pre-gif in the microsocope computer.