I don't see a disagreement here; I didn't say why I would rather see real
beads.  I agree that simulated data can be very useful, often preferable, in
controlling the variables of a problem when you are trying to make precise
quantitative determinations of how well a method is performing.  If such
measures are available, I want to know them.  However, the proof is still in
the puddin'--  I am not going to choose one method over another until I see
how they operate on real objects (that we know something about, of course)
on a real microscope.  And yes, beads (real beads) aren't the best sample in
all respects, as you have pointed out, but they are well-defined in terms of
size and index of refraction, and they are convenient.

And my eyes still seem to be working fairly well.

Cheers,
Jeff
Jeff Reece
Biomedical Engineer
Confocal Microscopy Center
National Institute for Environmental Health Sciences
P.O. Box 12233, MD F2-02
Research Triangle Park,  NC  27709
(919) 541-0311
[log in to unmask]


> ----------
> From:         Joachim Walter[SMTP:[log in to unmask]]
> Reply To:     Confocal Microscopy List
> Sent:         Wednesday, March 29, 2000 4:48 AM
> To:   [log in to unmask]
> Subject:      Re: Deconvolution software
>
> Jeff and others,
>
>
> > I would rather see real beads.
> >
>
> Sorry, but I don't agree on this point. Using simulated data has the
> advantage that you know exactly what is your input to the algorithm,
> thus enables you to judge how the algorithm treats different kinds of
> aberrations. E.g. you create an "ideal" object and can apply all kinds
> of PSFs (also spacially varying ones), noise, lamp/laser jitter, ...
> separately by software. If you take "real" data, you always get the same
> set of aberrations that the microscope(s) you use create(s).
> I think the data Andres shows is a step in the right direction. Still I
> have two comments:
>
> - Beads as test objects don't show everything. As MLE and similar
> algorithms are nonlinear processes, the quality of deconvolution should
> depend on what kind of object one looks on. Maybe over time the
> microscopy community can agree on what test objects are suitable (dots,
> rods, filaments, fractals, E-M images of cells, ...?) In the end one
> would have a generally accepted set of test data that everyone, who
> wants to test a deconvolution algorithm, can use.
> - It is hard to judge by eye how good a result is. What does it mean, if
> a bead looks a bit smaller after deconvolution? Does the algorithm just
> "eat" the borders (overreconstruct) or is this a sound regain of
> information? I would be much more confident to judge a result if I had a
> generally accepted figure of merit that tells me how good it is. Again,
> there will probably be several suitable figures of merit that all have
> their pros and cons. So one would like to apply them all to get a
> general impression. And again, one needs to use simulated data to be
> able to compare the deconvolution result to a real original.
>
> To give you an impression of what I mean I would like to draw your
> attention to the work of a collaborator of ours, Rainer Heintzmann.
> http://www.aphys.uni-heidelberg.de/AG_Cremer/rheintz/Dissertation/node55.h
> tml
> I have not been involved in this work, so this is no self advertisement.
> I just found myself in the situation of having to choose a deconvolution
> algorithm for our lab and having to rely on in a way subjective
> criteria.
>
> This mail is also a response to mails that Michael C. Wussow and Beat
> Ludin posted to several people off the list. Michael, Beat, would you
> like to post your mails to the list, again?
>
> Joachim
>
>
> --
> ------------------------------------------------------------------
> Joachim Walter, Dipl. Phys.
> Institut für Anthropologie und Humangenetik der LMU München
> AG Cremer
> Richard-Wagner-Straße 10/I
> D-80333 München               Tel. +49 - 89-2180-6713
> Germany                       Fax. +49 - 89-2180-6719
> ------------------------------------------------------------------
>