Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi everybody,

First of all many thanks for this great list that taught me so many tips
and tricks for microscopy. In our group, we do a lot of fluorescent
imaging using confocal or wide-field microscopy. We use ImageJ (great
plugin compilation by Tony Collins at WCIF) for image manipulation and
Volocity for deconvolution and rendering (very powerful software,
specially on a fast computer like our bipro G5 but a little bit "closed
black box" for me).

I spent hours (OK, tenths of minutes) searching the web for open-source
deconvolution & rendering solutions. As regards deconvolution, plugins
for ImageJ exist (like DeconvolutionJ from Nick Linnenbrügger or
Iterative Deconvolution from Bob Dougherty) but I could'nt get nice
results with my stacks, which are quite large (let's say 1000x1000x60).
XCOSM seems OK but I could'nt get it to work on either PC or Mac (I
stalled at the point of calculating a PSF). What about ORFMCOSM that's
supposed to replace XCOSM, do anybody have news ? (maybe Dr Conchello is
on this list ?).

The point is, we get nicer results with Volocity using calculated PSFs
than with experimental PSFs. I know this issue has been extensively
debated on this list, but the best measured PSFs I could get were not
good enough to meet calculated PSF performance. We ended up using a
calculated PSF that we fitted (in terms of objective NA) to the angle of
the measured PSF (the half angle of the light cone in XZ view is
matematically linkable to the objective NA).  The funny thing is that
our 100X, NA 1.4 Leica objective had a measured NA around 1.1 !
To cut things short, I really would like to find some piece of (free !)
software that can calculate PSFs in 3D and export them as TIFF stacks.
Volocity calculates PSFs but uses a proprietary format that is not
easily understandable (and good luck to get the specs of the "acff"
format...). I was wondering if someone uses or has heard about an ImageJ
plugin doing that ? I recently heard about Powermicroscope by A.
Diaspro, got a login but my stack was too big. In their Mic. Res. Tech.
paper for "Power up your microscope" (2004), A. Diaspro and his
colleagues showed nice images of calculated PSFs. Is it possible to get
the software that calculates those PSFs or to get PSF stacks from the
web-basd program ? Or is it from a commercial software ? Is
powermicroscope.com still active anyway (last "News" is from 2003...)?

Another thing : for open source rendering, VolumeJ and SurfaceJ for
ImageJ, freeware Huygens (with limited shadowed rendering) are nice, but
the best result I saw was Osirix for OSX that is for medical imaging but
can be used for microscopy stacks. I there some kind of equivalent free
software in the Windows world?

Thanks again for the list, I hope people can help a soon-to-be PhD
(postdoc, anyone ?) trough the deconvolution jungle.


Christophe Leterrier

PhD Student
Neuronal Receptors Dynamics
Neurobiology Lab
ESPCI-CNRS UMR 7637
10 rue Vauquelin 75005 Paris France
tel 33 1 40 79 51 84
fax 33 1 40 79 47 57
[log in to unmask]