[3dem] best practice question for ThermoFisher microscopes

[Matthijn VOS]

Dear David,

The column alignments are exactly what the name suggest, this is to align the column. In principle this is everything below the first cross-over of the FEG. The column alignments are very stable and in principle do not change. Especially for cryo-EM you should only have one column alignment file per high tension and this is mostly the highest HT you have on your microscope. There is very little reason to use a Krios at any other KV than 300 and a glacios at 200kV since the DED still have the highest DQE at higher HT. When the 100kV detectors come out this might be different, but for now the default is basically the highest kV of your system is optimal.

In principle the only thing that really changes over time is the FEG. Hence the first step of the column alignment which is the FEG can be separately store in the FEG register. You in general first load a column alignment and then load the most recent FEG register.

For MS applications it is often the case that different FEG settings might be used. For instance you might want to change the gun lens. In that case you need a slightly different FEG alignment for that GL and thus have a second FEG register. Since a different FEG setting also is often related to a different mode the FEG register has the option to also save the mode, stigmator settings and a few other options you can see in the flap out.

What users however started doing is to sometimes go as far as saving feg registers for a change in stigmator settings. OR any mode change also re-align the column. TFS engineers also sometimes have the "routine" of re-alignming the column over and over again with any change that is made. You then run the risk of getting wildgrow in alignment files and FEG registers.

So the way it I supposed to be: 1 alignment file for 1 HT. 1 FEG register for the most recent gun settings. IF you do not need to change your gun for different applications you do not need more that 1 FEG register! In cryo applications with a counting detector that only allows a relatively narrow dose rate for optimal performance this is normally only 1 GL setting and thus only 1 FEG register. A simple as possible! If you FEG changes over time, you run through ONLY the gun alignment ones and UPDATE the FEG register.

Any stigmmation, coma and direct tunings should be taken care of by the autofucntions, quickly before each new run.

Hope this helps

Cheers

Matthijn

From: 3dem <3dem-bounces at ncmir.ucsd.edu> On Behalf Of Morgan, David Gene
Sent: Thursday, May 4, 2023 10:22 PM
To: 3dem at ncmir.ucsd.edu
Subject: [3dem] best practice question for ThermoFisher microscopes

Hi,

I recently realized that different TFS service engineers have told us different things about best practices for using the FEG registers and alignment files on our Talos Arctica.  One of the engineers told us to use the FEG registers to store the current best FEG settings and to use a series of alignment files to store things like commonly used imaging conditions for different tasks.  Another engineer said to use FEG registers for both purposes.

Is there a general consensus on this, and if not, what do people think are the advantages of using one over the other?

Thanks in advance for any responses.

--
    politics is more difficult than physics.
                                             A. Einstein

            David Gene Morgan
        Electron Microscopy Center
             047E Simon Hall
             IU Bloomington
          812 856 1457 (office)
          812 856 3221 (3200)
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