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Hi Richard,</div>
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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:</div>
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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. </div>
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A few ideas on how to solve this or work around it:</div>
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<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">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
</span><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; color: rgb(0, 0, 0);">permanently</span><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">.</span></li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); list-style-type: "2) ";">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">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.<br>
</span></li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); list-style-type: "3) ";">
<div><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Prevent unlinking/retraction.
</span><span style="letter-spacing: normal; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 16px; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-weight: 400;">Our system also unlinks but
I am not sure if others face the same issue. </span><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">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. </span></div>
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Best,</div>
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Honkit and Mark</div>
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<div style="margin-right: 0px; margin-left: 0px;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><b>Mark Ebrahim</b>
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<p style="margin-right: 0px; margin-left: 0px;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Senior Staff Scientist</span></p>
<p style="margin-right: 0px; margin-left: 0px;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Cryo Electron Microscopy Resource Center (CEMRC)</span></p>
<div style="margin: 0px;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; color: rgb(0, 0, 0);">The Rockefeller University</span></div>
<div style="margin: 0px;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; color: rgb(0, 0, 0);">1230 York Avenue</span></div>
<div style="margin: 0px;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; color: rgb(0, 0, 0);">New York, NY 10065</span></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Walsh, Richard Michael <Richard_Walsh@hms.harvard.edu><br>
<b>Sent:</b> Saturday, January 20, 2024 7:56 AM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Subject:</b> [3dem] Calling Teamtomo: our CERES ICE-Shield isn't working properly</font>
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<td align="center"><b><font color="#AF1F0A" size="4">Caution: External email</font></b></td>
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<div class="x_elementToProof"><span style="letter-spacing:normal; font-family:Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(29,28,29); background-color:rgb(248,248,248); font-weight:400">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.</span></div>
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</span></div>
<div class="x_elementToProof"><span style="letter-spacing:normal; font-family:Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(29,28,29); background-color:rgb(248,248,248); font-weight:400">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.</span></div>
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<p class="x_elementToProof" style="margin-top:0px; margin-bottom:0px"><span style="font-family:Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">Link to Video For Reference:
</span><span style="letter-spacing:normal; font-family:Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(36,36,36); font-weight:400"><a href="https://urldefense.com/v3/__https://drive.google.com/file/d/1dyQR57ZPr6SQv_AypQvH-uOSCqPkD9jp/view__;!!Mih3wA!E4y-pfw8EsMkATaLFu-CyxAq6fvhvv2ObUTsGRwM7Zuf9I7SZj3gejlAO1pKmek9JdeXQL0L8NxOyAI8Sr8M5sPNdEuM68CYxg$" target="_blank" id="OWA960f675f-1cd8-e66e-71e9-3ee6205c6adc" class="x_OWAAutoLink" rel="noopener noreferrer" data-auth="NotApplicable" data-linkindex="0" style="margin:0px">https://drive.google.com/file/d/1dyQR57ZPr6SQv_AypQvH-uOSCqPkD9jp/view</a></span></p>
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<p class="x_elementToProof" style="margin-top:0px; margin-bottom:0px"><span style="font-family:Arial,Helvetica,sans-serif; font-size:12pt">So far neither Delmic nor ThermoFisher have any idea how to resolve this problem.</span></p>
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<p class="x_elementToProof" style="margin-top:0px; margin-bottom:0px">Any ideas would be greatly appreciated.</p>
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<p class="x_elementToProof" style="margin-top:0px; margin-bottom:0px">best regards,</p>
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<p class="x_elementToProof" style="margin-top:0px; margin-bottom:0px">Richard</p>
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<span style="font-family:Helvetica; font-size:12px">Richard M. Walsh , Ph.D.</span><br>
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<span style="font-family:Helvetica; font-size:12px">Managing Director</span></div>
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<span style="font-family:Helvetica; font-size:12px">The Harvard Cryo-EM </span><br>
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<span style="font-family:Helvetica; font-size:12px"><a href="mailto:Richard_Walsh@hms.harvard.edu" id="OWA4a736038-4223-4baf-c1bf-48774856dfc3" class="x_OWAAutoLink" data-loopstyle="linkonly" style="text-align:left">Email:Richard_Walsh@hms.harvard.edu</a></span><br>
<span style="font-family:Helvetica; font-size:12px">Web: <a href="https://urldefense.com/v3/__http://cryoem.hms.harvard.edu/__;!!Mih3wA!E4y-pfw8EsMkATaLFu-CyxAq6fvhvv2ObUTsGRwM7Zuf9I7SZj3gejlAO1pKmek9JdeXQL0L8NxOyAI8Sr8M5sPNdEuMOhc5rw$" id="OWA5fcabfef-cc5b-975e-1e7c-4a05be694db1" class="x_OWAAutoLink" data-loopstyle="linkonly" style="text-align:left">
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