[ome-users] install ome

[Curtis Rueden]

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

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
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