[3dem] magnification question
David Stokes
stokes at nyu.edu
Wed Jun 24 11:24:42 PDT 2020
Virtual pixel size (to go along with our virtual lives)
On 6/24/2020 2:22 PM, Jaap Brink wrote:
> 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
>>>>> 812 856 1457 (office)
>>>>> 812 856 3221 (3200)
>>>>> https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!X899ad5fpMrqAzCBPwtyOFe2YubIutVj4CG7FthqyO4QeWN6PMRCSuHgAtClFeRrjw$
>>>>> 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
>>>>>
>>>>> This message was sent from a non-IU address. Please exercise
>>>>> caution when clicking links or opening attachments from external
>>>>> sources.
>>>>>
>>>>> 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$
>>>>> _______________________________________________
>>>>> 3dem mailing list
>>>>> 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
>>>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwMGaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=hgbDG_ZdQaorZsucl01zHg&m=cEcSUVyDj3X-pLHwpkyLZBxuzvycXRrqaWwyndBoy3E&s=c4OVK_iOrXCbAzxIlJG-Fs7UGP1_Xp_6lwY_Rifhkkk&e=>
>>>>> _______________________________________________
>>>>> 3dem mailing list
>>>>> 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
>>>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwMGaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=hgbDG_ZdQaorZsucl01zHg&m=cEcSUVyDj3X-pLHwpkyLZBxuzvycXRrqaWwyndBoy3E&s=c4OVK_iOrXCbAzxIlJG-Fs7UGP1_Xp_6lwY_Rifhkkk&e=>
>>>>
>>>> _______________________________________________
>>>> 3dem mailing list
>>>> 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
>>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwMGaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=hgbDG_ZdQaorZsucl01zHg&m=cEcSUVyDj3X-pLHwpkyLZBxuzvycXRrqaWwyndBoy3E&s=c4OVK_iOrXCbAzxIlJG-Fs7UGP1_Xp_6lwY_Rifhkkk&e=>
>>>
>>> _______________________________________________
>>> 3dem mailing list
>>> 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwMGaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=hgbDG_ZdQaorZsucl01zHg&m=cEcSUVyDj3X-pLHwpkyLZBxuzvycXRrqaWwyndBoy3E&s=c4OVK_iOrXCbAzxIlJG-Fs7UGP1_Xp_6lwY_Rifhkkk&e=>
>>
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwMGaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=hgbDG_ZdQaorZsucl01zHg&m=cEcSUVyDj3X-pLHwpkyLZBxuzvycXRrqaWwyndBoy3E&s=c4OVK_iOrXCbAzxIlJG-Fs7UGP1_Xp_6lwY_Rifhkkk&e=>
>
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=hgbDG_ZdQaorZsucl01zHg&m=cEcSUVyDj3X-pLHwpkyLZBxuzvycXRrqaWwyndBoy3E&s=c4OVK_iOrXCbAzxIlJG-Fs7UGP1_Xp_6lwY_Rifhkkk&e=
--
David L. Stokes
Skirball Institute, Dept. of Cell Biology
NYU School of Medicine
https://urldefense.com/v3/__http://stokeslab.med.nyu.edu/__;!!Mih3wA!WNSATU1GeXC_aoNnHNxVODDnz1A8zvE_M9GWFWqNEIPqfH79Ra_8Q0geL7DVLYLNLg$
tel: 212-263-1580
fax: 212-263-2150
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200624/385ee618/attachment-0001.html>
More information about the 3dem
mailing list