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<p>For tomography I like to think of the field of view, which is relevant and obviously on the specimen, and the number of pixels in the image file. TEM, STEM, binning, whatever, the recorded scale is just the ratio of those two.<br>
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<p>For single particle the scale in nm/pixel is unambiguously on the sample.<br>
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<p>Detector (or camera) pixel size is just a number, in microns. One wouldn't really say the camera pixel size is 14 microns per pixel. The semantics make sense like this.</p>
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<p>best,</p>
<p>Michael<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Schmid, Michael F. <m-schmid@slac.stanford.edu><br>
<b>Sent:</b> Wednesday, June 24, 2020 9:25:08 PM<br>
<b>To:</b> Craig Yoshioka; Mike Strauss<br>
<b>Cc:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> Re: [3dem] magnification question</font>
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<span style="font-size:14.0pt">I usually just ask, “Hey, what’s your Å/pixel?”. I’m old-fashioned, though; I should really be asking “Hey, what’s your nm/pixel?” :-)<o:p></o:p></span></p>
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<span style="font-size:14.0pt">Since pixels are not that small (yet) on the detector, people usually know what I’m asking about.<o:p></o:p></span></p>
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<span style="font-size:14.0pt">Mike<o:p></o:p></span></p>
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<b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Craig Yoshioka <yoshiokc@ohsu.edu><br>
<b>Date: </b>Wednesday, June 24, 2020 at 11:19 AM<br>
<b>To: </b>Mike Strauss <mike.strauss@mcgill.ca><br>
<b>Cc: </b>"3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
<b>Subject: </b>Re: [3dem] magnification question<o:p></o:p></span></p>
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Hi Mike,<o:p></o:p></p>
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Yup- I also find myself many times saying “physical pixel size” only to realize right afterward the possibility for confusion. To add to that, when someone asks me about the “magnification", I will often respond with the ‘physical pixel size’ referring specifically
to the image pixel size at the detector's physical sampling rate (independent of image resampling/“binning”).
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This has been a recurring source of confusion, any suggestions for clarifying the nomenclature here?<o:p></o:p></p>
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On Jun 24, 2020, at 10:49 AM, Mike Strauss <<a href="mailto:mike.strauss@mcgill.ca" style="color: blue; text-decoration: underline;">mike.strauss@mcgill.ca</a>> wrote:<o:p></o:p></p>
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<span style="font-size:8.5pt;font-family:Menlo-Regular">I agree with Wim, magnification is not terribly useful by itself.<br>
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To clarify some terminology:<br>
<br>
detector pixel size - this is the size of the pixel on the chip. Eg. 14 um for a Falcon 3 camera, and 5 um for a K3<br>
image pixel size - the size this pixel represents in the image. If I understand him correctly, this is the calibrated pixel size Wim is talking about.<br>
<br>
In TEM, the magnification is determined by the ratio of the two. Mag = detector pixel size / image pixel size As a thought experiment - a microscope with a K3 mounted on the same plane as a Falcon 3 would give images of the same magnification, but would
sample the image plane differently (Field of view is different, and sampling frequency is different).<br>
<br>
The term “physical pixel size”, although common, is sometimes used to describe the image pixel size (as Wim did previously) and sometimes the detector pixel size (the physical dimensions of the pixels on the sensor chip). It is usually context that dictates
what is meant by physical pixel size, so be careful of this term<br>
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<br>
Regards,<br>
mike<br>
<br>
--------<br>
Mike Strauss<br>
Dep’t of Anatomy and Cell Biology<br>
McGill University<br>
3640 University St.<br>
Strathcona Anatomy Bldg, Rm 144<br>
Montreal, QC H3A 0C7<br>
(514) 398-8084<br>
</span><a href="mailto:mike.strauss@mcgill.ca" style="color: blue; text-decoration: underline;"><span style="font-size:8.5pt;font-family:Menlo-Regular">mike.strauss@mcgill.ca</span></a><span style="font-size:8.5pt;font-family:Menlo-Regular"><br>
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<span style="font-size:8.5pt;font-family:Menlo-Regular">On 24. Jun 2020, at 10:37, Wim Hagen <<a href="mailto:hagen@embl.de" style="color: blue; text-decoration: underline;">hagen@embl.de</a>> wrote:<br>
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Hi,<br>
<br>
In the old days with film cameras, when the screen went up, the indicated magnification changed to reflect the magnification at the film camera plane. Any digital camera mounted below that plane would thus get a post-magnification, typically 1.4x for Philips/FEI/TFS
instruments. Without film cameras (Glacios, Arctica, Krios) this behaviours has at some point been removed from the software. As stated by others, magnification is the worst thing to use as a parameter, we should just stick to calibrated physical pixel size
of the detector.<span style=""> </span><br>
<br>
Wim Hagen<br>
EMBL Heidelberg<br>
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<span style="font-size:8.5pt;font-family:Menlo-Regular">On 24. Jun 2020, at 15:58, Morgan, David Gene <<a href="mailto:dagmorga@indiana.edu" style="color: blue; text-decoration: underline;">dagmorga@indiana.edu</a>> wrote:<br>
<br>
Hi,<br>
<br>
Several people have reported what Zongli said about the mag changing when the screen is inserted. This does _not_ happen with our Artica and I think that it does not happen with most/all Glacios/Artica/Krios TEM's. Either ThermoFisher has deliberately
turned off this behavior, or it is another bug in recent release of the software.<br>
<br>
--<span style=""> </span><br>
politics is more difficult than physics.<br>
A. Einstein<br>
<br>
David Gene Morgan<br>
Electron Microscopy Center<br>
047E Simon Hall<br>
IU Bloomington<br>
812 856 1457 (office)<br>
812 856 3221 (3200)<br>
<a href="https://urldefense.com/v3/__http:/iubemcenter.indiana.edu__;!!Mih3wA!X899ad5fpMrqAzCBPwtyOFe2YubIutVj4CG7FthqyO4QeWN6PMRCSuHgAtClFeRrjw$" style="color: blue; text-decoration: underline;">https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!X899ad5fpMrqAzCBPwtyOFe2YubIutVj4CG7FthqyO4QeWN6PMRCSuHgAtClFeRrjw$</a><span style=""> </span><br>
From: Michael Elbaum <<a href="mailto:michael.elbaum@weizmann.ac.il" style="color: blue; text-decoration: underline;">michael.elbaum@weizmann.ac.il</a>><br>
Sent: Wednesday, June 24, 2020 3:20 AM<br>
To: Zongli Li; Morgan, David Gene<br>
Cc:<span style=""> </span><a href="mailto:3dem@ncmir.ucsd.edu" style="color: blue; text-decoration: underline;">3dem@ncmir.ucsd.edu</a><br>
Subject: [External] Re: [3dem] magnification question<br>
<br>
This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.<br>
<br>
Just a heads-up then... I was shocked to see that the magnification written into a file name by the Talos software depends on the size of the monitor attached. Maybe this is STEM-specific? It's very misleading. Altogether magnification is a slippery concept
though. The pixel sampling is much less ambiguous: what length in the specimen does a pixel in the recorded file represent? Multiply by the number of pixels for the field of view. It's the same image whether you view on your phone or projected onto the wall.<br>
<br>
Michael<br>
From: 3dem <<a href="mailto:3dem-bounces@ncmir.ucsd.edu" style="color: blue; text-decoration: underline;">3dem-bounces@ncmir.ucsd.edu</a>> on behalf of Zongli Li <<a href="mailto:zongli.li@gmail.com" style="color: blue; text-decoration: underline;">zongli.li@gmail.com</a>><br>
Sent: Tuesday, June 23, 2020 11:38:26 PM<br>
To: Morgan, David Gene<br>
Cc:<span style=""> </span><a href="mailto:3dem@ncmir.ucsd.edu" style="color: blue; text-decoration: underline;">3dem@ncmir.ucsd.edu</a><br>
Subject: Re: [3dem] magnification question<br>
<br>
Hi David Gene,<br>
<br>
The magnifications reported by a Talos Arctica user interface should be " mag on the viewing screen" if the viewing screen is inserted, and will change to " mag on the CCD" when viewing screen is extracted. But as Sacha pointed out, what matters is really the
calibrated mag on the whatever camera you have used for calibration and data collection, and this mag will not show up in the user interface, but stored in the magnification table in Gatan GMS if you are using Gatan CCD/K2/K3 camera.<br>
<br>
Best,<br>
<br>
Zongli<br>
<br>
On Tue, Jun 23, 2020 at 1:50 PM Morgan, David Gene <<a href="mailto:dagmorga@indiana.edu" style="color: blue; text-decoration: underline;">dagmorga@indiana.edu</a>> wrote:<br>
Hi,<br>
<br>
Does anyone happen to know whether the magnifications reported by a Talos Artica are supposed to be "mag on the viewing screen" or "mag at the film plane"? We clearly have a serious issue with the calibrated magnifications on our microscope, but I just
recalibrated it and got more or less the same lousy magnifications. I'm trying to understand our issues, and knowing what the microscope thinks it is reporting would be helpful. Thanks in advance.<br>
<br>
--<span style=""> </span><br>
politics is more difficult than physics.<br>
A. Einstein<br>
<br>
David Gene Morgan<br>
Electron Microscopy Center<br>
047E Simon Hall<br>
IU Bloomington<br>
812 856 1457 (office)<br>
812 856 3221 (3200)<br>
<a href="https://urldefense.com/v3/__http:/iubemcenter.indiana.edu__;!!Mih3wA!X899ad5fpMrqAzCBPwtyOFe2YubIutVj4CG7FthqyO4QeWN6PMRCSuHgAtClFeRrjw$" style="color: blue; text-decoration: underline;">https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!X899ad5fpMrqAzCBPwtyOFe2YubIutVj4CG7FthqyO4QeWN6PMRCSuHgAtClFeRrjw$</a><span style=""> </span><br>
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