[ome-users] Problems with OME-Server and WND-CHARM

[Curtis Rueden]

Hi Joachim,

On 6 April 2009 07:53:30 BST, Joachim Beig <beigjoach at fh-bingen.de> wrote:

Dear Sir or Madam, my name is Joachim Beig, I'm a German student of
bioinformatics at the University Of Applied Sciences, Fachhochschule Bingen,
Germany. At the moment I'm working on my diploma thesis which is about
Feature Extraction of Microscopy Images, and therefore I want to install the
OME-Server to check out the WND-CHARM software packet. Sadly, it seems that
there was a change in the CURL-library, so a environment-variable called
"CURL_MUTE" isn't found from the installation routine and I'm not able to go
further. (I tried to install OME Server on Ubuntu 8.10 and Fedora 10,
unfortunately I have no Mac or Fedora 4...) So I want to ask you if there is
a chance to get the source-code of this packages to hava just a look on it?
I think it's just a Matlab-Code, isn't it? Or is there a way to get support
for installing the OME-Server? I'm looking forward to hearing from you! Best
regards! Joachim Beig


I suggest you give the standalone WND-CHARM written in C a try. Ilya
Goldberg recently commented on using WND-CHARM, both the standalone version
and the one integrated with OME Server. I have included his instructions
below. If you have further questions, feel free to write again to the OME
users list.

HTH,
Curtis

Ilya Goldberg wrote:

It depends what you want to do.  There are two options right now:
1) run WND-CHARM to see if it works for your particular experimental system
(i.e. use just the pattern recognition algorithm)
To do this all you need is the wndchrm utility which you can download here:
http://ome.grc.nia.nih.gov/wnd-charm/wndchrm-1-26.tar.gz
The only requirements for this utility are the FFTW library and the libtiff
library.
LibTIFF: http://www.libtiff.org
FFTW 3.1: http://www.fftw.org/download.html
You don't need any OME or OMERO bits to run this.

The utility is installed using the regular "./configure; make; sudo make
install" set of commands.  It will check for the presence of its required
libraries and fail during the configure step if it can't find them.
There is a fairly detailed usage manual for this utility published here:
http://www.scfbm.org/content/3/1/13
You can also get a usage message by just executing wndchrm without any
parameters.
Very briefly, it relies on a set of folders full of images, each folder
defining a training class.  It trains itself on the set of folders you
provide, and generates a set of HTML reports describing how well it can
distinguish the different classes, their relative similarities, etc.

This utility is designed to have many instances of itself running
concurrently on the same set of images.  We use it in the lab on a cluster
of a dozen computers each with 2-8 cores, all sharing the same drive.  Then
we launch the utility with the same command line as many times as there are
cores/CPUs available.  In other words, its not just a demo utility - we use
it regularly in the lab to do science.
This is all very manual, but its pretty straight-forward to set up and get
running without a lot of conceptual overhead.

2) Set up OME to run with MATLAB and the MATLAB-based WND-CHARM.
This is quite a bit more involved, but I can help you through this if that's
what you want to do.  This type of system is more geared to people who are
using MATLAB to develop new image analysis algorithms.  It can also be used
to run WND-CHARM on a cluster, and we've used it in this mode quite a bit.
The problem with this set up is that MATLAB likes changing its APIs with
every minor version release (every 6 months or so), and its become
increasingly difficult to keep up.  Probably the future is to use the more
stable Java API for MATLAB and do this through OMERO.  MATLAB's various DRM
schemes and licensing shenanigans are making this a less attractive way to
go with each passing release.  Still, its heavily used and is well supported
by OMERO, with "best effort" support by OME.

The third option, which is not available right now, is to get a complete,
integrated OME/OMERO/WND-CHARM in an easily installable tidy package without
MATLAB requirements.
That's obviously what we want to provide as soon as we can, but we're not
there yet.

You can contact Lior or myself if we can help you further.
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