[3dem] magnification question

Wed Jun 24 11:22:59 PDT 2020

Hi all,

Hm,  what about sample pixel size?

Regards,
Jaap

On Jun 24, 2020, at 1:19 PM, Craig Yoshioka <yoshiokc at ohsu.edu> wrote:

Hi Mike,

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”).

This has been a recurring source of confusion, any suggestions for clarifying the nomenclature here?

On Jun 24, 2020, at 10:49 AM, Mike Strauss <mike.strauss at mcgill.ca<mailto:mike.strauss at mcgill.ca>> wrote:

I agree with Wim, magnification is not terribly useful by itself.

To clarify some terminology:

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
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.

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).

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

Regards,
mike

--------
Mike Strauss
Dep’t of Anatomy and Cell Biology
McGill University
3640 University St.
Strathcona Anatomy Bldg, Rm 144
Montreal, QC H3A 0C7
(514) 398-8084
mike.strauss at mcgill.ca<mailto:mike.strauss at mcgill.ca>

On 24. Jun 2020, at 10:37, Wim Hagen <hagen at embl.de<mailto:hagen at embl.de>> wrote:

Hi,

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.

Wim Hagen
EMBL Heidelberg

On 24. Jun 2020, at 15:58, Morgan, David Gene <dagmorga at indiana.edu<mailto:dagmorga at indiana.edu>> wrote:

Hi,

   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.

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

           David Gene Morgan
       Electron Microscopy Center
            047E Simon Hall
            IU Bloomington
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         812 856 3221 (3200)
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From: Michael Elbaum <michael.elbaum at weizmann.ac.il<mailto:michael.elbaum at weizmann.ac.il>>
Sent: Wednesday, June 24, 2020 3:20 AM
To: Zongli Li; Morgan, David Gene
Cc: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
Subject: [External] Re: [3dem] magnification question

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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.

Michael
From: 3dem <3dem-bounces at ncmir.ucsd.edu<mailto:3dem-bounces at ncmir.ucsd.edu>> on behalf of Zongli Li <zongli.li at gmail.com<mailto:zongli.li at gmail.com>>
Sent: Tuesday, June 23, 2020 11:38:26 PM
To: Morgan, David Gene
Cc: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] magnification question

Hi David Gene,

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.

Best,

Zongli

On Tue, Jun 23, 2020 at 1:50 PM Morgan, David Gene <dagmorga at indiana.edu<mailto:dagmorga at indiana.edu>> wrote:
Hi,

   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.

--
   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)
     https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!X899ad5fpMrqAzCBPwtyOFe2YubIutVj4CG7FthqyO4QeWN6PMRCSuHgAtClFeRrjw$<https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!X899ad5fpMrqAzCBPwtyOFe2YubIutVj4CG7FthqyO4QeWN6PMRCSuHgAtClFeRrjw$>
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