online microscope calculator (iScopeCalc)

[Talley Lambert]

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Hi all,

I've been working on a microscope calculator web-app.  At the risk of presenting something well below
the expertise level of the average reader here, I'd like to share it with you!  At the very least, I'm
hoping it might be of educational use for students of microscopy… if not also of practical use for
microscope users.

It is primarily designed as a widefield/spinning disk calculator and should be useful in assessing
sampling rate and/or confocality in a variety of optical setups.  The calculator takes a variety of inputs
related to your optical setup, and pumps out values for things like lateral resolution, axial resolution,
sampling rate, field of view, amount of camera chip used, etc…  It includes the ability to calculate Airy
Units and confocality with adjustable pinhole systems such as the Yokogawa W1, or the Borealis mod
from Spectral.  It has chip parameters for many of the more popular cameras so you can quickly
determine the appropriate settings (with binning or optical relays) to achieve Nyquist sampling with your
given camera. There is also a graphical representation of a diffraction limited point source for quick
visualization of the current settings.

The calculator is designed to be easily viewed on a desktop browser (though support for Internet
Explorer 8 or earlier is weak) or as an app on a mobile device such as an iPhone or iPad.  You can also
save configurations for later recall (which might be useful in a core setting with a number of fixed
configurations).

Here is the link:

http://iscopecalc.com

If you like it, please use it and share it!  I would LOVE to hear your thoughts and ideas for improvement
or complaints about bugs or inaccuracies!  Feel free to contact me directly.

Thanks!
-Talley

~~~~~~~~~~~
Talley Lambert, PhD
Dept. VCAPP
Washington State University
tlambert [at] vetmed.wsu.edu

[Arne Seitz]

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"I'm hoping it might be of educational use for students of microscopy. if not also of practical use for microscope users."

In order to be of educational use it would be desirable if basic physical principals of optics would have been taken into account. Your tool allows to calculate the resolution for air objectives with a NA of 1.5. Also glycerol und water objectives with that NA are tolerated. The unit of your sampling rate is pixel. But these are only minor details.

My main criticism: which model did you use to calculate all these fancy numbers?  You just present a black-box which is spitting out numbers. This is to my understanding neither of educational nor of scientific use.

It is maybe a nice toy but nothing which helps to advance the understanding of microscopy. This is not meant to be personally against you. Probably you are a very talented programmer for web-apps. But I doubt that you have been ever involved in teaching of how to use a microscope properly.

Or am I just a little bit too old-fashioned....

Best regards
Arne


---------------------------------------------------------------
Arne Seitz
Head of Bioimaging and Optics Platform (BIOP)
Swiss Institute of Technology (EPFL)
Faculty of Life Sciences
Station 15
CH-1015 Lausanne

Phone: [phone]
Fax:      [phone]
http://biop.epfl.ch/
---------------------------------------------------------------

 

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Talley Lambert
Sent: jeudi 21 février 2013 20:50
To: [hidden email]
Subject: online microscope calculator (iScopeCalc)

*****
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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi all,

I've been working on a microscope calculator web-app.  At the risk of presenting something well below the expertise level of the average reader here, I'd like to share it with you!  At the very least, I'm hoping it might be of educational use for students of microscopy. if not also of practical use for microscope users.

It is primarily designed as a widefield/spinning disk calculator and should be useful in assessing sampling rate and/or confocality in a variety of optical setups.  The calculator takes a variety of inputs related to your optical setup, and pumps out values for things like lateral resolution, axial resolution, sampling rate, field of view, amount of camera chip used, etc.  It includes the ability to calculate Airy Units and confocality with adjustable pinhole systems such as the Yokogawa W1, or the Borealis mod from Spectral.  It has chip parameters for many of the more popular cameras so you can quickly determine the appropriate settings (with binning or optical relays) to achieve Nyquist sampling with your given camera. There is also a graphical representation of a diffraction limited point source for quick visualization of the current settings.

The calculator is designed to be easily viewed on a desktop browser (though support for Internet Explorer 8 or earlier is weak) or as an app on a mobile device such as an iPhone or iPad.  You can also save configurations for later recall (which might be useful in a core setting with a number of fixed configurations).

Here is the link:

http://iscopecalc.com

If you like it, please use it and share it!  I would LOVE to hear your thoughts and ideas for improvement or complaints about bugs or inaccuracies!  Feel free to contact me directly.

Thanks!
-Talley

~~~~~~~~~~~
Talley Lambert, PhD
Dept. VCAPP
Washington State University
tlambert [at] vetmed.wsu.edu

[Talley Lambert]

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Arne,

Thanks for your feedback!
To answer your main criticism: if you click on menu at the top, you'll see a
selection called "equations" and there can see all of the equations used to
calculate those fancy numbers :) . . . I don't like black boxes either!

yes, I admit, I haven't programmed in the appropriate constraints in the user
interface for the NA limits of various mounting media, I'll do that!  thanks for
pointing that out.  and I agree that "pixels" is not the appropriate unit for
sampling rate... I have removed it.  (in truth, the number represents the number
of pixels packed into one Raxial) ...

sorry to hear you see it as just a toy!  I do really care about microscopy, I am
involved in teaching microscopy, and I'm not really a programmer at all (this is
my first go...).  It's still a work in progress so I hope I haven't insulted you with
my first attempt!  If at all possible, I'd love to make it somewhat useful.  so do
keep the suggestions coming...

cheers,
-Talley

[Arne Seitz]

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Talley,

I don't want to insult you either. And maybe my criticism was a little bit too harsh.
My very personal opinion is the following: such calculators are a toy because they are of limited practical use. Whenever I'm asked what about the resolution of a wide-field microscope, I answer: laterally: half of the emission wavelength divided through the NA of the objective; for confocal microscopes the axial resolution is 3-4 times bigger than the lateral resolution. This is something which you can easily remember. And you do not need any tools to calculate it. Just basic math. And once you know this relationship you have learned something.
I know that my numbers are not totally correct. But in practice this is completely irrelevant. At least in 95% of the cases. And if you need to have more precise numbers you should also make sure that the model you are using is valid. And then everything is getting much more complicated anyway....

But as I already said: maybe I'm just old fashioned.

Regards
Arne


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Talley Lambert
Sent: jeudi 21 février 2013 23:47
To: [hidden email]
Subject: Re: online microscope calculator (iScopeCalc)

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Arne,

Thanks for your feedback!
To answer your main criticism: if you click on menu at the top, you'll see a selection called "equations" and there can see all of the equations used to calculate those fancy numbers :) . . . I don't like black boxes either!

yes, I admit, I haven't programmed in the appropriate constraints in the user interface for the NA limits of various mounting media, I'll do that!  thanks for pointing that out.  and I agree that "pixels" is not the appropriate unit for sampling rate... I have removed it.  (in truth, the number represents the number of pixels packed into one Raxial) ...

sorry to hear you see it as just a toy!  I do really care about microscopy, I am involved in teaching microscopy, and I'm not really a programmer at all (this is my first go...).  It's still a work in progress so I hope I haven't insulted you with my first attempt!  If at all possible, I'd love to make it somewhat useful.  so do keep the suggestions coming...

cheers,
-Talley

[Gabriel Lapointe-4]

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Hi Arne,
Seems like a tool full of potential. Unfortunately it has a very limited
use since it can't be customized to other scope or dies. The posibility to
had specific numerical value would greatly increase it's possibility..

*Gabriel Lapointe, M.Sc.*
Lab Manager / Microscopy Specialist
Concordia University, Biology Department
7141 Sherbrooke St. West SP 534
Montréal QC H4B 1R6 Canada
Lab : [phone] x5988
Office : [phone] x3008
Fax : [phone]
Cell : [phone]
[hidden email]
cmac.concordia.ca
http://gabriellapointe.ca


2013/2/21 Talley Lambert <[hidden email]>

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Arne,
>
> Thanks for your feedback!
> To answer your main criticism: if you click on menu at the top, you'll see
> a
> selection called "equations" and there can see all of the equations used to
> calculate those fancy numbers :) . . . I don't like black boxes either!
>
> yes, I admit, I haven't programmed in the appropriate constraints in the
> user
> interface for the NA limits of various mounting media, I'll do that!
>  thanks for
> pointing that out.  and I agree that "pixels" is not the appropriate unit
> for
> sampling rate... I have removed it.  (in truth, the number represents the
> number
> of pixels packed into one Raxial) ...
>
> sorry to hear you see it as just a toy!  I do really care about
> microscopy, I am
> involved in teaching microscopy, and I'm not really a programmer at all
> (this is
> my first go...).  It's still a work in progress so I hope I haven't
> insulted you with
> my first attempt!  If at all possible, I'd love to make it somewhat
> useful.  so do
> keep the suggestions coming...
>
> cheers,
> -Talley
>

[Talley Lambert]

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Hi Gabriel,

Thanks for the response.  There are definitely some inherent limitations in there.  
I guess I'm trying to find a balance between ease of use and functionality.  I
could easily open up some of the controls to make them fully user-editable, (more
like the NA slider for example).  Which inputs would you most like to have more
control over?  

I'm thinking a direct input for the emission wavelength (rather than a drop down
menu) is the first thing to add...  what else would you like to see?

thanks again for having a look!
-Talley

[George McNamara]

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Hi Talley,

Top right quadrant (with pukey green background) - and "show details"
section - has a hideously ugly 1980s computer font. The equations page
also has font/text sizes - especially subscripts - that are unreadable.

The green blob in the pixels field does not do much for me. You have a
lot of 'drak gray space' underneath the "show graphic" - would be much
more useful to show an intensity profile. Even better: TWO intensity
profiles, one for XY, one for XZ (plenty of drak gray space at lower
left for XZ). You don't explain to the user - anywhere - what the green
blob represents.

Your "show details" for default settings for widefield has "Depth of
field" values - that change depending on camera!

To me, the "standard of care" in biomedical fluorescence microscopy is
missing: pinhole 1 Airy unit confocal laser scanning microscope. This
could be generic.

George
p.s. EGFP ex/em 488/509 nm ... implies ~1 nm emission band. While this
is doable on the www.lightforminc.com PARISS (along with a whole lot of
other wavelengths), ~1 nm is not realistic on the microscopes you are
modeling. I suggest you think about the consequences of using real
emission bandpasses on emission spectra, and the consquences for the
resolution equations that include emission wavelengths.


On 2/21/2013 5:47 PM, Talley Lambert wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Arne,
>
> Thanks for your feedback!
> To answer your main criticism: if you click on menu at the top, you'll see a
> selection called "equations" and there can see all of the equations used to
> calculate those fancy numbers :) . . . I don't like black boxes either!
>
> yes, I admit, I haven't programmed in the appropriate constraints in the user
> interface for the NA limits of various mounting media, I'll do that!  thanks for
> pointing that out.  and I agree that "pixels" is not the appropriate unit for
> sampling rate... I have removed it.  (in truth, the number represents the number
> of pixels packed into one Raxial) ...
>
> sorry to hear you see it as just a toy!  I do really care about microscopy, I am
> involved in teaching microscopy, and I'm not really a programmer at all (this is
> my first go...).  It's still a work in progress so I hope I haven't insulted you with
> my first attempt!  If at all possible, I'd love to make it somewhat useful.  so do
> keep the suggestions coming...
>
> cheers,
> -Talley
>
>    

[Steffen Dietzel]

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Talley,

my main criticism is that it is not working. I use Firefox 18, for
saftey reasons with NoScript and Flashblocker.

Clearly I have to allow scripts from iscopecalc.com but why is it
required to allow scripts from three more web sites including
google-analytics? I don't like that. Even if I allow them all and allow
Flash "for this Website" it still doesn't work. For cases like that I
have an "open" Win Explorer and there it seems to be fine.
Other than that, since I don't have a spinning disk but a point scanner,
It would be nice to be able to freely define pixel/voxel size and
pinhole size.

Cheers

Steffen



On 21.02.2013 20:49, Talley Lambert wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi all,
>
> I've been working on a microscope calculator web-app.  At the risk of presenting something well below
> the expertise level of the average reader here, I'd like to share it with you!  At the very least, I'm
> hoping it might be of educational use for students of microscopy… if not also of practical use for
> microscope users.
>
> It is primarily designed as a widefield/spinning disk calculator and should be useful in assessing
> sampling rate and/or confocality in a variety of optical setups.  The calculator takes a variety of inputs
> related to your optical setup, and pumps out values for things like lateral resolution, axial resolution,
> sampling rate, field of view, amount of camera chip used, etc…  It includes the ability to calculate Airy
> Units and confocality with adjustable pinhole systems such as the Yokogawa W1, or the Borealis mod
> from Spectral.  It has chip parameters for many of the more popular cameras so you can quickly
> determine the appropriate settings (with binning or optical relays) to achieve Nyquist sampling with your
> given camera. There is also a graphical representation of a diffraction limited point source for quick
> visualization of the current settings.
>
> The calculator is designed to be easily viewed on a desktop browser (though support for Internet
> Explorer 8 or earlier is weak) or as an app on a mobile device such as an iPhone or iPad.  You can also
> save configurations for later recall (which might be useful in a core setting with a number of fixed
> configurations).
>
> Here is the link:
>
> http://iscopecalc.com
>
> If you like it, please use it and share it!  I would LOVE to hear your thoughts and ideas for improvement
> or complaints about bugs or inaccuracies!  Feel free to contact me directly.
>
> Thanks!
> -Talley
>
> ~~~~~~~~~~~
> Talley Lambert, PhD
> Dept. VCAPP
> Washington State University
> tlambert [at] vetmed.wsu.edu
>

--
------------------------------------------------------------
Steffen Dietzel, PD Dr. rer. nat
Ludwig-Maximilians-Universität München
Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
Head of light microscopy

Mail room:
Marchioninistr. 15, D-81377 München

Building location:
Marchioninistr. 27,  München-Großhadern

[Talley Lambert]

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Hi Steffen,

Yeah, the whole app is a javascript app, so, as you have found, disabling
javascript will completely break the app.  Sorry, I wouldn't be able to do it as a
web-app without using javascript (and I don't know much about making native
apps, java applets, or flash-based apps).  But I totally understand the desire for
security, so here's all the scripts and what they do (flash is not required by the
way):

Required:

iscopecalc.com/js/calc.js
this is the main script file that I wrote that runs the calculator and controls all of
the interactions and calculations.

http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.js
this is the jQuery javascript library (being served from a google content delivery
network), used on about half of the websites on the internet, including google,
amazon, etc....  it is basically just a way for me to more easily interact with the
HTML document.  you can learn more at http://jquery.com

http://code.jquery.com/mobile/1.3.0/jquery.mobile-1.3.0.min.js
this is the jQuery mobile library.  it is required for forming the interface of the
calculator and is also required. you can learn more at http://jquerymobile.com

Optional:

mathjax.org
this script used to render the equations listed on the equations page.  you can
disable it but the equations will look like mumbo-jumbo...

google-analytics.com
basic usage statistics such as browser type and such are indeed sent to google
analytics.  however, this is totally optional and you can either block this with
noscript, or, if you like you can use the URL www.iscopecalc.com/?analytics=off  
which will not send any information to google analytics.

That said, using Firefox 19 with NoScript installed, I am able to successfully use
the calculator with both mathjax and google analytics disabled (as long as
jquery, jquerymobile, and iscopecalc are allowed).  So, if you are still unable to
use it with Firefox after enabling those three required scripts, please email me
directly, as I'd like to figure out what the problem might be.

With regards to laser scanning calculations... I'm not exactly sure what the
purpose of the calculator would be if you had the freedom that a LSM provides
and can set the pixel and pinhole size as you desire.  Are there calculations that
are not done automatically for you that you'd like to see included?  If you can
just set pinhole to 1 AU and chose an arbitrary pixel size appropriate for nyquist
sampling... what is the need for a calculator?

thanks for writing!
-Talley




On Tue, 26 Feb 2013 17:50:25 +0100, Steffen Dietzel <[hidden email]>
wrote:

>*****
>To join, leave or search the confocal microscopy listserv, go to:
>http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>*****
>
>Talley,
>
>my main criticism is that it is not working. I use Firefox 18, for
>saftey reasons with NoScript and Flashblocker.
>
>Clearly I have to allow scripts from iscopecalc.com but why is it
>required to allow scripts from three more web sites including
>google-analytics? I don't like that. Even if I allow them all and allow
>Flash "for this Website" it still doesn't work. For cases like that I
>have an "open" Win Explorer and there it seems to be fine.
>Other than that, since I don't have a spinning disk but a point scanner,
>It would be nice to be able to freely define pixel/voxel size and
>pinhole size.
>
>Cheers
>
>Steffen
>
>
>
>On 21.02.2013 20:49, Talley Lambert wrote:
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Hi all,
>>
>> I've been working on a microscope calculator web-app.  At the risk of

presenting something well below
>> the expertise level of the average reader here, I'd like to share it with you!  
At the very least, I'm
>> hoping it might be of educational use for students of microscopy… if not also
of practical use for
>> microscope users.
>>
>> It is primarily designed as a widefield/spinning disk calculator and should be
useful in assessing
>> sampling rate and/or confocality in a variety of optical setups.  The
calculator takes a variety of inputs
>> related to your optical setup, and pumps out values for things like lateral
resolution, axial resolution,
>> sampling rate, field of view, amount of camera chip used, etc…  It includes
the ability to calculate Airy
>> Units and confocality with adjustable pinhole systems such as the Yokogawa
W1, or the Borealis mod
>> from Spectral.  It has chip parameters for many of the more popular
cameras so you can quickly
>> determine the appropriate settings (with binning or optical relays) to achieve
Nyquist sampling with your
>> given camera. There is also a graphical representation of a diffraction
limited point source for quick
>> visualization of the current settings.
>>
>> The calculator is designed to be easily viewed on a desktop browser (though
support for Internet
>> Explorer 8 or earlier is weak) or as an app on a mobile device such as an
iPhone or iPad.  You can also
>> save configurations for later recall (which might be useful in a core setting
with a number of fixed
>> configurations).
>>
>> Here is the link:
>>
>> http://iscopecalc.com
>>
>> If you like it, please use it and share it!  I would LOVE to hear your thoughts
and ideas for improvement

>> or complaints about bugs or inaccuracies!  Feel free to contact me directly.
>>
>> Thanks!
>> -Talley
>>
>> ~~~~~~~~~~~
>> Talley Lambert, PhD
>> Dept. VCAPP
>> Washington State University
>> tlambert [at] vetmed.wsu.edu
>>
>
>
>--
>------------------------------------------------------------
>Steffen Dietzel, PD Dr. rer. nat
>Ludwig-Maximilians-Universität München
>Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
>Head of light microscopy
>
>Mail room:
>Marchioninistr. 15, D-81377 München
>
>Building location:
>Marchioninistr. 27,  München-Großhadern