[ome-users] question re bioformats.jar

[Curtis Rueden]

Hi Keith,

Sorry for the delay in my response; I was out sick on Friday. I can't
speak to your question #2, but have some thoughts on #1 and #3.

> 1) we are not able to import any type of images other than TIF, (for
> example leica format)
>
> As OME is installed in /OME and is owned by user OME, we have tried putting
> the LOCI bioformats.jar in the OME directory, or in Java/lib and neither
> seem to change things.  I don't know how to change the classpath of the OME
> user, as it doesn't have a home directory, thus a .cshrc etc... to add the
> classpath to its environment...
>
> Any hints?

Unfortunately, Bio-Formats is not so integrated with the OME server
yet. Ultimately, we may include the Bio-Formats JARs with OME, or
allow them to be dropped into the distribution as you tried, and have
the perl code automatically attempt to use them. But such
functionality is not yet in place.

The OME server is perl-based, with several file format importers on
the backend, written in Perl (modules in
OME/src/perl2/OME/ImportEngine), including: Bio-Rad PIC, DICOM,
Deltavision DV, Molecular Dynamics GEL, Zeiss LSM, Metamorph HTD,
OME-TIFF, Metamorph STK, TIFF, and OME-XML.

Bio-Formats is Java-based, with many file format readers implemented
(see the Bio-Formats web site:
http://www.loci.wisc.edu/ome/formats.html). But we have not fully
integrated Bio-Formats with the OME server.

Currently, the easiest way to get files supported by Bio-Formats into
OME is to use the OME Plugin for ImageJ
(http://www.loci.wisc.edu/ome/imagej.html). But even though
Bio-Formats is capable of producing OME-XML metadata for each file,
the OME Plugin only supports upload of pixel data to the server. We
are actively working to improve this support, but there is still much
to be done.

There is also a command line tool called omeul packaged with VisBio,
which we are in the middle of refactoring into Bio-Formats directly.
If you need to batch upload many files to OME, you could try
downloading VisBio and using the packaged version of omeul; it should
be able to upload pixel data in any supported file format.

> 3) in regards to accessing the images from a browser on a second machine,
> the images are refered to by a url pointing to the image file which works
> on the host machine, but not on the second machine.  How do you set OME to
> use a relative not absolute link to the images?

I am not certain, but this sounds like an issue with the path to your
OMEIS (since OMEIS is what provides the thumbnails). The OME database
needs the full hostname to OMEIS, even if it is on the same machine
(which it is by default). Did you specify a complete URL to OMEIS when
it prompted in the installer? You can check as follows (assuming you
are logged in with the account used to install OME):

% psql ome
Welcome to psql 8.0.7, the PostgreSQL interactive terminal.

Type:  \copyright for distribution terms
       \h for help with SQL commands
       \? for help with psql commands
       \g or terminate with semicolon to execute query
       \q to quit

ome=# select * from repositories;
 attribute_id | module_execution_id |                 image_server_url
                | path | is_local
--------------+---------------------+--------------------------------------------------+------+----------
            4 |                   1 |
http://skyking.microscopy.wisc.edu/cgi-bin/omeis |      | f
(1 row)

And if necessary, you can update the URL like so:

ome=# update repositories set
image_server_url='http://skyking.microscopy.wisc.edu/cgi-bin/omeis'
where module_execution_id=1;
UPDATE 1
ome=# \q
%

-Curtis

On 10/13/06, Keith.Neil at sanofi-aventis.com
<Keith.Neil at sanofi-aventis.com> wrote:
> I have 3 questions regarding OME on OSX 10.4 (intel)
>
> 1) we are not able to import any type of images other than TIF, (for
> example leica format)
>
> As OME is installed in /OME and is owned by user OME, we have tried putting
> the LOCI bioformats.jar in the OME directory, or in Java/lib and neither
> seem to change things.  I don't know how to change the classpath of the OME
> user, as it doesn't have a home directory, thus a .cshrc etc... to add the
> classpath to its environment...
>
> Any hints?
>
> 2) we would like to have a Samba mount to a network disk in the OME_images
> directory we created in the default user home in OSX.  We can do this on
> osx by creating an alias to the samba mount.  Problem is this is not
> recognised by the Apache browser.  I imagine we can create a symlink to the
> network mount, but I haven't done this osx before...
>
> 3) in regards to accessing the images from a browser on a second machine,
> the images are refered to by a url pointing to the image file which works
> on the host machine, but not on the second machine.  How do you set OME to
> use a relative not absolute link to the images?
>
> Thanks for any help.
>
> Keith
>
>
> ------------------------------
> Le présent message ainsi que ses éventuelles pièces jointes est
> exclusivement destiné au(x) destinataire(s), personnes physiques ou
> morales, qu'il désigne.
> Il constitue de ce fait une correspondance à caractère privé et peut
> contenir des informations confidentielles.
> Si ce message vous est parvenu par erreur, nous vous remercions d'en aviser
> immédiatement l'expéditeur par retour de ce courrier électronique puis de
> le détruire, ainsi que ses éventuellement pièces jointes, sans en conserver
> de copie.
>
> This message, including any attachment, is intended for the use of the
> individual or entity to which it is addressed.
> It is therefore to be considered as a private correspondence which may
> contain confidential information.
> If you are not the intended recipient, please advise the sender immediately
> by reply e.mail and delete this message and any attachment thereto without
> retaining a copy.
> ------------------------------
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>