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Virtual pixel size (to go along with our virtual lives)<br>
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<div class="moz-cite-prefix">On 6/24/2020 2:22 PM, Jaap Brink wrote:<br>
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<blockquote type="cite"
cite="mid:E27075DF-0952-4719-BC7A-19BFF1DF69DD@jeol.com">
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Hi all,
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<div>Hm, what about sample pixel size?<br>
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<div><br>
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<div>Regards,</div>
Jaap</div>
<div dir="ltr"><br>
<blockquote type="cite">On Jun 24, 2020, at 1:19 PM, Craig
Yoshioka <a class="moz-txt-link-rfc2396E" href="mailto:yoshiokc@ohsu.edu"><yoshiokc@ohsu.edu></a> wrote:<br>
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<div class="">Hi Mike,</div>
<div class=""><br class="">
</div>
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”).
<div class=""><br class="">
</div>
<div class="">This has been a recurring source of confusion,
any suggestions for clarifying the nomenclature here?<br
class="">
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""><br class="">
<div class=""><br class="">
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<div class=""> <br class="">
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<blockquote type="cite" class="">
<div class="">On Jun 24, 2020, at 10:49 AM,
Mike Strauss <<a
href="mailto:mike.strauss@mcgill.ca"
class="" moz-do-not-send="true">mike.strauss@mcgill.ca</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="caret-color: rgb(0,
0, 0); font-family: Menlo-Regular;
font-size: 11px; font-style: normal;
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normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none; float: none;
display: inline !important;" class="">I
agree with Wim, magnification is not
terribly useful by itself.</span><br
style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
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text-align: start; text-indent: 0px;
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text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none; float: none;
display: inline !important;" class="">To
clarify some terminology:</span><br
style="caret-color: rgb(0, 0, 0);
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11px; font-style: normal;
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normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
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word-spacing: 0px;
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text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none; float: none;
display: inline !important;" class="">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</span><br
style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none; float: none;
display: inline !important;" class="">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.</span><br
style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none; float: none;
display: inline !important;" class="">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).</span><br style="caret-color:
rgb(0, 0, 0); font-family: Menlo-Regular;
font-size: 11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none; float: none;
display: inline !important;" class="">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</span><br
style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none; float: none;
display: inline !important;" class="">Regards,</span><br
style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
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text-decoration: none; float: none;
display: inline !important;" class="">mike</span><br
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normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none; float: none;
display: inline !important;" class="">--------</span><br
style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
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normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
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<span style="caret-color: rgb(0, 0, 0);
font-family: Menlo-Regular; font-size:
11px; font-style: normal;
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text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
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display: inline !important;" class="">Mike
Strauss</span><br style="caret-color:
rgb(0, 0, 0); font-family: Menlo-Regular;
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<span style="caret-color: rgb(0, 0, 0);
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of Anatomy and Cell Biology</span><br
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<span style="caret-color: rgb(0, 0, 0);
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University</span><br style="caret-color:
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University St.</span><br
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<span style="caret-color: rgb(0, 0, 0);
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Anatomy Bldg, Rm 144</span><br
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<span style="caret-color: rgb(0, 0, 0);
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QC H3A 0C7</span><br style="caret-color:
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<span style="caret-color: rgb(0, 0, 0);
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398-8084</span><br style="caret-color:
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<a href="mailto:mike.strauss@mcgill.ca"
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On 24. Jun 2020, at 10:37, Wim Hagen <<a
href="mailto:hagen@embl.de" class=""
moz-do-not-send="true">hagen@embl.de</a>>
wrote:<br class="">
<br class="">
Hi,<br class="">
<br class="">
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
class="Apple-converted-space"> </span><br
class="">
<br class="">
Wim Hagen<br class="">
EMBL Heidelberg<br class="">
<br class="">
<blockquote type="cite" class="">On 24.
Jun 2020, at 15:58, Morgan, David Gene
<<a
href="mailto:dagmorga@indiana.edu"
class="" moz-do-not-send="true">dagmorga@indiana.edu</a>>
wrote:<br class="">
<br class="">
Hi,<br class="">
<br class="">
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
class="">
<br class="">
--<span class="Apple-converted-space"> </span><br
class="">
politics is more difficult than
physics.<br class="">
A. Einstein<br class="">
<br class="">
David Gene Morgan<br class="">
Electron Microscopy Center<br
class="">
047E Simon Hall<br class="">
IU Bloomington<br class="">
812 856 1457 (office)<br
class="">
812 856 3221 (3200)<br class="">
<a
href="https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!X899ad5fpMrqAzCBPwtyOFe2YubIutVj4CG7FthqyO4QeWN6PMRCSuHgAtClFeRrjw$"
class="" moz-do-not-send="true">https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!X899ad5fpMrqAzCBPwtyOFe2YubIutVj4CG7FthqyO4QeWN6PMRCSuHgAtClFeRrjw$</a><span
class="Apple-converted-space"> </span><br
class="">
From: Michael Elbaum <<a
href="mailto:michael.elbaum@weizmann.ac.il"
class="" moz-do-not-send="true">michael.elbaum@weizmann.ac.il</a>><br
class="">
Sent: Wednesday, June 24, 2020 3:20 AM<br
class="">
To: Zongli Li; Morgan, David Gene<br
class="">
Cc:<span class="Apple-converted-space"> </span><a
href="mailto:3dem@ncmir.ucsd.edu"
class="" moz-do-not-send="true">3dem@ncmir.ucsd.edu</a><br
class="">
Subject: [External] Re: [3dem]
magnification question<br class="">
<br class="">
This message was sent from a non-IU
address. Please exercise caution when
clicking links or opening attachments
from external sources.<br class="">
<br class="">
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
class="">
<br class="">
Michael<br class="">
From: 3dem <<a
href="mailto:3dem-bounces@ncmir.ucsd.edu"
class="" moz-do-not-send="true">3dem-bounces@ncmir.ucsd.edu</a>>
on behalf of Zongli Li <<a
href="mailto:zongli.li@gmail.com"
class="" moz-do-not-send="true">zongli.li@gmail.com</a>><br
class="">
Sent: Tuesday, June 23, 2020 11:38:26 PM<br
class="">
To: Morgan, David Gene<br class="">
Cc:<span class="Apple-converted-space"> </span><a
href="mailto:3dem@ncmir.ucsd.edu"
class="" moz-do-not-send="true">3dem@ncmir.ucsd.edu</a><br
class="">
Subject: Re: [3dem] magnification
question<br class="">
<br class="">
Hi David Gene,<br class="">
<br class="">
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
class="">
<br class="">
Best,<br class="">
<br class="">
Zongli<br class="">
<br class="">
On Tue, Jun 23, 2020 at 1:50 PM Morgan,
David Gene <<a
href="mailto:dagmorga@indiana.edu"
class="" moz-do-not-send="true">dagmorga@indiana.edu</a>>
wrote:<br class="">
Hi,<br class="">
<br class="">
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
class="">
<br class="">
--<span class="Apple-converted-space"> </span><br
class="">
politics is more difficult than
physics.<br class="">
A. Einstein<br class="">
<br class="">
David Gene Morgan<br class="">
Electron Microscopy Center<br
class="">
047E Simon Hall<br class="">
IU Bloomington<br class="">
812 856 1457 (office)<br
class="">
812 856 3221 (3200)<br class="">
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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<br>
<pre class="moz-signature" cols="72">--
David L. Stokes
Skirball Institute, Dept. of Cell Biology
NYU School of Medicine
<a class="moz-txt-link-freetext" href="https://urldefense.com/v3/__http://stokeslab.med.nyu.edu/__;!!Mih3wA!WNSATU1GeXC_aoNnHNxVODDnz1A8zvE_M9GWFWqNEIPqfH79Ra_8Q0geL7DVLYLNLg$">http://stokeslab.med.nyu.edu/</a>
tel: 212-263-1580
fax: 212-263-2150
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