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Regarding localization accuracy in super-resolution imaging: Alex Small and I wrote a review recently summarizing and explaining the theory underlying it, and describing its practical implementation in various algorithms: http://www.annualreviews.org/doi/abs/10.1146/annurev-physchem-040513-103735
Feel free to email me if you can't access the PDF. ([log in to unmask])
Relatedly, some 2D tools, with MATLAB code, including simulated images and a GUI for various algorithms (including mine!) are here: http://physics-server.uoregon.edu/~raghu/particle_tracking.html
best wishes,
Raghu
--
Raghuveer Parthasarathy
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Group web page: http://physics.uoregon.edu/~raghu/
Blog: http://eighteenthelephant.wordpress.com/
Associate Professor
Department of Physics
1274 University of Oregon
Eugene, OR 97403-1274
http://physics.uoregon.edu/~raghu/
On Wednesday, March 5, 2014 12:58 AM, Christophe Leterrier <[log in to unmask]> wrote:
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Thank you for all these informative answers!
The Holtzer et al. article is providing a formula for Z-loclaization
precision in the astigmatism case (although they have a x2 factor between
theory and simulation because they don't explicitely take pixelation into
account).
I also found this recent article:
Rieger B, Stallinga S. The Lateral and Axial Localization Uncertainty in
Super-Resolution Light Microscopy. Chemphyschem. 2013 Dec 2. doi:
10.1002/cphc.201300711. [Epub ahead of print] PubMed PMID: 24302478.
http://onlinelibrary.wiley.com/doi/10.1002/cphc.201300711/abstract
Here they explicitly approximate the Z-localization precision of biplane,
astigmatism and double-helix modalities, taking into account pixelation and
background with a claimed <1% error. Although I don't really understand the
formulas yet, because they depend on the "the distance between focal lines"
and "a measure of the focal depth" that are "obtained by a calibration
measurement" but not explicited further it seems.
Thanks again,
Christophe
2014-03-04 23:33 GMT+01:00 Zdenek Svindrych <[log in to unmask]>:
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi,
>
> also a brute force simulation of many images of many molecules and
> subsequent localisation with your preferred method is a straightforward
> (albeit a bit time consuming) way to get the localisation accuracy (and
> precision...) at nearly real-life conditions. You can simulate any photon
> counts, background, detector pixelation, effect of molecule density, biases
> of the localisation algos and so on.
>
> Hopefully our group (Guy Hagen et al) will soon publish a software tool to
> greatly simplify this. But I still didn't find a satisfactory astigmatic
> PSF
> model to include into the simulation. The cylindrical gaussian is really
> not
> close approximation of our experimental results...
>
> Best,
>
> zdenek svindrych
> lf1.cuni.cz
>
>
>
> ---------- Původní zpráva ----------
> Od: Sripad Ram <[log in to unmask]>
> Komu: [log in to unmask]
> Datum: 4. 3. 2014 23:17:16
> Předmět: Re: discussion is open...continues ... about localization and
> super
> resolution
>
> "*****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi Chris,
> The z-localization precision for astigmatism based 3D localization was
> worked out by holtzer et al., applied physics letters, 2007, 90, 053902.
>
> On a related note, the precise calculations for the X/Y localization
> precision that includes background and pixilation was published in 2004 by
> Raimund Ober group (Ober et al; Biophysical Journal, 2004, 86:1185-1200).
> You can download the software to calculate the localization precision from
> here (http://www.wardoberlab.com/software/fandplimittool/).
>
> Hope this helps.
>
> Regards,
> Sripad
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[log in to unmask]]
> On
> Behalf Of Christophe Leterrier
> Sent: Tuesday, March 04, 2014 3:16 PM
> To: [log in to unmask]
> Subject: Re: discussion is open...continues ... about localization and
> super
> resolution
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> This is a great introduction to a question a wanted to ask to the SMLM
> specialists (I did not find the answer in the above reference). I also
> posted it on the Nanoscopy LinkedIn group, so I'm sorry for people that
> will
> get it two times!
>
> There are several formulas to estimate the lateral (XY) precision of
> individual localization events in PALM/STORM microscopy. This goes from the
> crude sigma(PSF)/√Nphotons to more elaborate formulas that includes
> pixelation and background (such as Thomson & Webb Biophys J 2002, corrected
> in Mortensen Nat Methods 2010). What I'm looking for is an equation that
> allows to estimate the precision for the Z localization when using
> astigmatism-based 3D PALM/STORM. The reference I have found where this
> precision is studied theoretically (such as Badierostami Applied Phys Lett
> 2010, Shaevitz Int J Optics 2009) do not use a directly calculable formula.
>
> I assume the precision depends on the photon number and the point on the Z
> calibration curve with the respective X and Y PSF width. Is anyone aware of
> such a formula?
>
> Best Regards,
>
> Christophe
>
>
>
>
> 2014-03-04 21:52 GMT+01:00 Alberto Diaspro <[log in to unmask]>:
>
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > *****
> >
> > http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2843.html
> >"
>
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