Re: Light Lab by Carl Zeiss Microscopy for iOS devices - SVI Nyquist Calculator

Posted by Steffen Dietzel on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Light-Lab-by-Carl-Zeiss-Microscopy-for-iOS-devices-tp7184469p7195537.html

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Cameron,

thank you for sharing this link, a nice tool indeed.

Maybe I didn't have enough coffee yet, but it appears that although the
PSF is visualized and Nyquist is calculatet, the FWHM (or 'resolution')
is not given.

A pitty, in particular since their Nyquist values multiplied by 2.3 and
what I have calculated don't really match (in multi-photon examples).

But I don't have the time right now to check which formulas they have
applied.

Steffen


On 16.01.2012 22:57, Cameron Nowell wrote:

> Ok for some reason it didn’t let me post my first response so here it is again
>
> Hi Steffen,
>
> The SVI website has a Nyquist calculator that does what you want
>
> http://www.svi.nl/NyquistCalculator
>
>
> It calculates optimal Nyquist for various settings. It can also generate a PSF of a refractive mismatch to show you what goes wrong if you want. It seems to be limited to<10um into your sample though for some reason.
>
> The calculations for resolution at different depths is easy enough to code up for a webpage, but the brightness shift is rather tricky. There are so many parameters that will effect the brightness of your fluorophore as you go deeper into your sample (even in a perfectly matched situation) that I don't think it would be possible to calculate it. You could get a theoretical value but I doubt it would reflect reality in any way in an actual tissue or clump of cells.
>
> If anyone knows of some formulas to do these sort of calculations send em through and I can put a calculator up on my facilities webpage.
>
>
> Cheers
>
> Cam
>
>
> Cameron J. Nowell
> Microscopy Manager
> Centre for Advanced Microscopy
> Ludwig Institute for Cancer Research Melbourne - Parkville Branch PO Box 2008 Royal Melbourne Hospital Victoria, 3050 AUSTRALIA
> Office: [phone]
> Mobile: [phone]
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>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cameron Nowell
> Sent: Tuesday, 17 January 2012 8:26 AM
> To: [hidden email]
> Subject: Re: Light Lab by Carl Zeiss Microscopy for iOS devices
>
> One other thing, the calculator asks for the back projected pinhole size. You can calculate that here http://www.svi.nl/BackprojectedPinholeCalculator
>
>
> Cheers
>
> Cam
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Steffen Dietzel
> Sent: Tuesday, 17 January 2012 12:06 AM
> To: [hidden email]
> Subject: Re: Light Lab by Carl Zeiss Microscopy for iOS devices
>
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>
> Well, for my part I wouldn't mind an (Android) app for
>
> - z-resolution, prefereably one that includes 2- and 3-photon excitation and
>
> - resolution and brightness at various depths under refraction index mismatch conditions (e.g. sample embedded in glycerol instead of immersion oil or underneath a coverslip with a dipping objective).
>
> Life isn't always as simple as 0.61 lambda/NA.
>
>
> Even better though than a bunch of apps for various systems would a calculator running in a web browser based on common standards so that it would be accessible on every system.
>
>
> Steffen
>
>
> On 16.01.2012 02:08, Guy Cox wrote:
>> There isn't any difference between widefield and confocal resolution in any normal fluorescence mode.   Do you really need an app to work out 0.61 lambda/NA?  And then to divide by 2.3 to get Nyquist?  If you are in multiphoton it's a little more complicated since root 2 (1.414) comes in, but you can just use the formula 0.43 lambda / NA.
>>
>> Guy
>>
>> Optical Imaging Techniques in Cell Biology
>> by Guy Cox    CRC Press / Taylor&   Francis
>>        http://www.guycox.com/optical.htm
>> ______________________________________________
>> Guy Cox, MA, DPhil(Oxon), Honorary Associate, Australian Centre for
>> Microscopy&   Microanalysis, Madsen Building F09, University of Sydney,
>> NSW 2006
>>
>> Phone [phone]     Fax [phone]
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>
>
> --
> ------------------------------------------------------------
> Steffen Dietzel, PD Dr. rer. nat
> Ludwig-Maximilians-Universität München
> Walter-Brendel-Zentrum für experimentelle Medizin (WBex) Head of light microscopy
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--
------------------------------------------------------------
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