[ome-users] install ome

[josh.moore at gmx.de]

Curtis Rueden writes:
 > Hi John,

Hi John,

 > Thanks for your inquiry. I am replying to the OME users list since it is
 > generally the best place to ask questions and receive support.
 > 
 > WND-CHARM currently exists in two forms: 1) a MATLAB-driven version
 > integrated with the OME Perl server, and 2) a more recent pure C/C++
 > version. There is currently no capability for the OMERO platform to interact
 > with WND-CHARM, though we plan to explore such a linkage in a future
 > release. There has also been discussion of potentially integrating WND-CHARM
 > with CellProfiler.
 > 
 > You can find the WND-CHARM documentation on the OME site, but unfortunately
 > it focuses on the older MATLAB-based version, and does not provide
 > standalone download links (the MATLAB version is bundled with the OME Perl
 > server download):
 > http://www.openmicroscopy.org/site/documents/data-management/ome-server/using-ome-server/automated-image-classification

The C/C++ version is available on the OME trac at:

  http://trac.openmicroscopy.org.uk/ome/browser/trunk/src/C/WND_CHARM

or via SVN at:

  http://svn.openmicroscopy.org.uk/svn/ome/trunk/src/C/WND_CHARM/

Getting the code working is straight-forward autotools, though you
will need the fftw3 library installed. With a much older version of
the OMERO C++ binding, I had investigated loading files from the
server. But since the command line version works very neatly with
directories of images, there's no immediate need.

Hope that helps,
~J.

 > Personally I would advise against using the MATLAB+OME version of WND-CHARM,
 > because we can offer only limited support for the OME Perl server, as our
 > efforts are now focused on the OMERO platform.
 > 
 > Unfortunately, I do not have a download link for the C/C++ version -- I'm
 > not sure whether it has been made publicly available yet. Ilya Goldberg's
 > group at NIA developed WND-CHARM, so hopefully someone there can comment
 > further on the status of WND-CHARM, its availability for download, and its
 > future directions.
 > 
 > -Curtis
 > 
 > On Thu, Feb 26, 2009 at 2:18 PM, John McLaughlin <jmclaughlin at rigel.com>wrote:
 > 
 > Hi, I am trying to install the OME platform so that I can try out the
 > wnd-charm analysis tool. I've made extended failed attempts with both the
 > omero platform and a linux version. I'd like to get some help or
 > suggestions. Who is the best person to contact? For a bit of background I
 > appear to be having trouble in the final steps due to problems that appear
 > to be related to ome interacting with postgres. I suspect I need to line up
 > my versions of ome, postgres, matlab etc. to get this example working (if it
 > can work of course). I've been through the OME website looking for help and
 > documentation regarding what versions of everything to use, but find the
 > information to be a bit vague and scattered about. For example after I got
 > ome working I realized I had to use the cvs ome version to get wnd-charm
 > working. After starting over I ran into permission issues with postgres
 > trying to run 'pollen' example. I tried a new version of postgresql
 > (8.3.6-1-linux) then ran into more password issues during final steps of the
 > install.pl script. Hard-coding in user names and passwords to the
 > Delegate.pm script cleared up some problems, but others appeared later and
 > it seemed like a good time to stop and ask for help. Thanks for your help
 > and time, John McLaughlin Rigel Pharmaceuticals, Inc South San Francisco, CA
 > 94080
 > _______________________________________________
 > ome-users mailing list
 > ome-users at lists.openmicroscopy.org.uk
 > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users