[3dem] Calling Teamtomo: our CERES ICE-Shield isn't working properly

Tue Jan 23 13:16:48 PST 2024

Thank you all for your suggestions!

We adjusted the speed of the insertion based on your feedback.

Excited to have this working properly.

best regards

Richard

Richard M. Walsh , Ph.D.

Managing Director
The Harvard Cryo-EM
Center for Structural Biology

Harvard Medical School
250 Longwood Avenue
SGM 102
Boston MA 02115

Phone: (617) 432-9042
Email:Richard_Walsh at hms.harvard.edu<mailto:Richard_Walsh at hms.harvard.edu>
Web: cryoem.hms.harvard.edu<https://urldefense.com/v3/__http://cryoem.hms.harvard.edu/__;!!Mih3wA!AYCPdIUV47upLd9H591kORHY2zgoY7pCVXZPLXc7XWeeoEdcdMugmcUmkE8ZuReYEC8xDOCywiiZ_oWOLvtEqV4IAxhAUKDHcA$ >
________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of sebastiantacke at freenet.de <sebastiantacke at freenet.de>
Sent: Tuesday, January 23, 2024 3:35 AM
To: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] Calling Teamtomo: our CERES ICE-Shield isn't working properly

Hello everyone,

Unfortunately, I accidentally sent my reply only to Richard but I agree with Sabrina, Honkit and Mark.

Attached my answer:

---

Dear all, Dear Richard,

I would suggest to increase (or decrease) the speed of shutter insertion.
You can do this on your own by opening one of the valve at the shutter a bit more.

But be gentle and test with small increments since you don’t want your shutter to fly in with warp 9 ;-)

If this doesn’t help, I would decrease the speed of shutter insertion by turning the valve the other way round.

There might be a small shift between the reference image and the following images but typically AutoTEM can correct for this.
If you need a picture of the valve or if you have any further questions, just let me know!

Have a nice Sunday.

Best wishes,

Sebastian

---

Happy milling and have a nice week.

Best wishes,

Sebastian

Von: 3dem <3dem-bounces at ncmir.ucsd.edu> Im Auftrag von Mark Ebrahim
Gesendet: Montag, 22. Januar 2024 19:40
An: Walsh, Richard Michael <Richard_Walsh at hms.harvard.edu>; 3dem at ncmir.ucsd.edu
Cc: Honkit Ng <hng at rockefeller.edu>
Betreff: Re: [3dem] Calling Teamtomo: our CERES ICE-Shield isn't working properly

Hi Richard,

Honkit (my research support specialist and Aquilos guru) and I were discussing this in the morning. We watched your video which was very helpful and noticed the following:

At about 7 seconds into the video the Z unlinks, this is what causes the ice shield to retract. When the stage is done moving, the Z re-links and about 18 seconds into the video the ice shield starts reinserting. The ice shield isn't fully inserted until the 22 second mark. However, the image acquisition takes place at the 20 second mark. i.e. the first half of the image is taken while the shield is still out of the field of view and the second half (just noise) is somewhere in the middle of insertion.

A few ideas on how to solve this or work around it:

  1.  The simplest workaround is to retake the image immediately after the shield is fully inserted. This should work and you can carry on until someone from either company is able to solve the issue permanently.
  2.  We would try to increase the rate of insertion such that the shield is fully inserted before the reference image is taken. By the looks of the video, the insertion needs to be about 3 seconds faster or the imaging could be delayed by 3-4 seconds.
  3.  Prevent unlinking/retraction. Our system also unlinks but I am not sure if others face the same issue. It may be argued this is done as a safety feature but we don't really see a significant risk here. As long as the stage is not moved up, there is no risk and this would not be required at this point in the workflow. It would make more sense to only retract if a Z stage movement is called. Additionally, it would make more sense to just get a pole touch instead of retracting the shield at all. Honkit noted that if the shield happened to crash into the stage, you would get no touch alarm but if the stage moves into the shield you would get a touch alarm i.e. you only get touch alarms when the stage is being called to move. So, it makes sense to us to just leave the shield inserted and get a touch alarm if the stage ever came into contact with the shield.

Best,

Honkit and Mark

________________________________

Mark Ebrahim

Senior Staff Scientist

Cryo Electron Microscopy Resource Center (CEMRC)

The Rockefeller University

1230 York Avenue

New York, NY 10065

________________________________

From: 3dem <3dem-bounces at ncmir.ucsd.edu<mailto:3dem-bounces at ncmir.ucsd.edu>> on behalf of Walsh, Richard Michael <Richard_Walsh at hms.harvard.edu<mailto:Richard_Walsh at hms.harvard.edu>>
Sent: Saturday, January 20, 2024 7:56 AM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: [3dem] Calling Teamtomo: our CERES ICE-Shield isn't working properly

Caution: External email

We have heard of several sites using the CERES Ice-Shield on their Aquilos with no issues, but we have a reoccurring problem, during the thinning stage and its effecting our lamella quality.

When using the CERES Ice-Shield in tandem with AutoTEM, we notice that each time the stage moves, the ice shield retracts and re-inserts, and thus during the thinning stage of the AutoTEM automation, the shield blocks reference image collection, thus resulting in a misplaced pattern and inconsistent lamella quality.

Link to Video For Reference: https://urldefense.com/v3/__https://drive.google.com/file/d/1dyQR57ZPr6SQv_AypQvH-uOSCqPkD9jp/view__;!!Mih3wA!AYCPdIUV47upLd9H591kORHY2zgoY7pCVXZPLXc7XWeeoEdcdMugmcUmkE8ZuReYEC8xDOCywiiZ_oWOLvtEqV4IAxhc2MJK-w$ <https://urldefense.com/v3/__https:/drive.google.com/file/d/1dyQR57ZPr6SQv_AypQvH-uOSCqPkD9jp/view__;!!Mih3wA!E4y-pfw8EsMkATaLFu-CyxAq6fvhvv2ObUTsGRwM7Zuf9I7SZj3gejlAO1pKmek9JdeXQL0L8NxOyAI8Sr8M5sPNdEuM68CYxg$>

So far neither Delmic nor ThermoFisher have any idea how to resolve this problem.

Any ideas would be greatly appreciated.

best regards,

Richard

Richard M. Walsh , Ph.D.

Managing Director

The Harvard Cryo-EM

Center for Structural Biology

Harvard Medical School
250 Longwood Avenue
SGM 102
Boston MA 02115

Phone: (617) 432-9042
Email:Richard_Walsh at hms.harvard.edu<mailto:Richard_Walsh at hms.harvard.edu>
Web: cryoem.hms.harvard.edu<https://urldefense.com/v3/__http:/cryoem.hms.harvard.edu/__;!!Mih3wA!E4y-pfw8EsMkATaLFu-CyxAq6fvhvv2ObUTsGRwM7Zuf9I7SZj3gejlAO1pKmek9JdeXQL0L8NxOyAI8Sr8M5sPNdEuMOhc5rw$>
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