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

Tue Jan 23 00:35:28 PST 2024

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!F0jyC8svnXql3ug6jMNB6DmFuHniYb0_VWw86RAZhVpnmGMBB3gEHcGO7Fh4GyTURYrsIDX_9ZyTUeLiDhSg7QqUWv6sGw$ 
<https://urldefense.com/v3/__https:/drive.google.com/file/d/1dyQR57ZPr6SQv_A
ypQvH-uOSCqPkD9jp/view__;!!Mih3wA!E4y-pfw8EsMkATaLFu-CyxAq6fvhvv2ObUTsGRwM7Z
uf9I7SZj3gejlAO1pKmek9JdeXQL0L8NxOyAI8Sr8M5sPNdEuM68CYxg$> 

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-pf
w8EsMkATaLFu-CyxAq6fvhvv2ObUTsGRwM7Zuf9I7SZj3gejlAO1pKmek9JdeXQL0L8NxOyAI8Sr
8M5sPNdEuMOhc5rw$> 

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