Re: software for fluorescence microscopy
Charles Plessy wrote:
> Dear Angus,
>
> You do not need to vote for inclusion of software on the list, because
> it is a wiki :)
Understood. I was hoping for some agreement that they were not too
general to be suitable for inclusion, before trying the wiki.
> Did you write front-ends in your laboratory? Easy to use
> frontends are what I think are missing in the field of fluorescence
> microscopy. In my previous lab, we had a nice set of Tk intefaces for
> easy merging or separation of RGB channels, but unfortunately it was
> never released.
No, we don't generally write front-ends - we tend to be too pushed for
time to do anything beyond getting the algorithms working in code, and
rely on command-line interface to work them.
Closely related though, perldl works very nicely with the visualisation
suite karma (http://www.atnf.csiro.au/computing/software/karma/) by
Richard Gooch, which is not packaged for debian, as far as I'm aware,
but is easily installable by rsync. I'm very slowly developing something
like that for numpy/scipy using wxPython, but it's nowhere near ready
for sharing with the world yet.
> I am currently considering to write a simple web interface to
> imagemagick, but I am suspecting that this is not the most
> ressource-efficient, nor the most portable accross Win / Mac / Unix.
> Actually, I already started, but if you have some programs to share,
> I'll be happy to stop and do something else.
Imagemagick certainly has a great set of tools, but I'm not convinced
that a web interface is the way to go either. Perhaps using the python
or perl programming interfaces, and a cross-platform GUI toolkit (like
wx) would be a good way to go. Ideally, this would also make it possible
to pull the images into the respective data language (perldl or numpy)
for more in-depth analysis if necessary, getting the best of both
worlds. How does that credo go: make the commonplace tasks simple and
the difficult ones possible?
A.
--
Angus McMorland
email a.mcmorland@auckland.ac.nz
mobile +64-21-155-4906
PhD Student, Neurophysiology / Multiphoton & Confocal Imaging
Physiology, University of Auckland
phone +64-9-3737-599 x89707
Armourer, Auckland University Fencing
Secretary, Fencing North Inc.
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