[ome-devel] Import/Export

[Curtis Rueden]

To those interested in VisBio:

>A plug for our partners at VisBio (http://www.loci.wisc.edu/visbio/):
>The 3.0 alpha version of VisBio has support for several more file formats, and can talk directly to OME.  You can download it here:
>http://www.loci.wisc.edu/visbio/alpha.html
>(Hope I'm not being too forward, Curtis and Kevin)

The current VisBio alpha is v3.00 alpha2. It does indeed support uploading data from VisBio to an OME database, with a couple of caveats; in particular, it needs a perl script called "StandaloneServer.pl" to be running on the server side. You can execute this with the commands:

   cd OME/src/perl2/OME/Remote
   perl StandaloneServer.pl -t xmlrpc -f -n -p 8002

Then in VisBio, for the server field, use the string:
   http://ip.address.of.ome:8002/

Where "ip.address.of.ome" is the IP address pointing to your OME installation.

I have recently been informed that the StandaloneServer approach to communication with the OME database is actually obsolete, and there is an easier method. Thus, VisBio v3.00 alpha3 will remove the need to execute this script, and allow you to specify your OME server simply as "ip.address.of.ome" without all the colons, slashes, ports, etc.

Expect v3.00 alpha3 before the end of August.

As for file formats: VisBio v3.00 alpha2 currently supports Bio-Rad PIC, uncompressed TIFF stacks, QuickTime movies, and Olympus Fluoview TIFF formats. The next alpha release will add support for Metamorph STK format. Also in the works are LZW-compressed TIFF, OpenLab LIF, Zeiss LSM, Leica, PerkinElmer, and Nikon formats.

This is an online help topic that describes how to upload to OME as well.

Lastly, we have plans to improve this upload capability to allow for batch uploading, to speed the import process.

If you have any questions or comments, feel free to let me know.

-Curtis