Open Microscopy Environment

Is there an OMERO module/package that would allow a user, from terminal, to make a connection to an omero database and retrieve images?

Ivan

Hi Ivan,

What are you intending to do? What do you mean by "retrieve images"? Do you want 2D JPGs? Do you mean OME "Images"? Assuming the latter, you can do:

Code: Select all

bin/omero export -f 1.ome.tiff Image:1


If you would like to see how that works from the API, see lib/python/omero/plugins/export.py.

Cheers,
~Josh

you know that with omeromatlab i can make a connection to an omero.server and retrieve images. i wonder if there is an omero python module/package that does the same. that is, something that allows me to make a connection say from my laptop to an omero.server and grab the images i want.

ivan

There is indeed:

http://trac.openmicroscopy.org.uk/ome/wiki/OmeroPy
http://trac.openmicroscopy.org.uk/ome/w ... tBeginners

two more questions
1) the current license allows me to modify omeropy?
2) this package requires Ice to be installed on the system. I've had problem installing Ice on Mac. I know about the posts in the forum and the website. But so far I've had no luck installing it on my Mac. Do you have a clue as to why? I've given up but I would like to know if you have an idea regarding this issue.

icaoberg wrote:two more questions
1) the current license allows me to modify omeropy?

The GPL license is used for all OMERO code, including OMERO.py. This allows you to make whatever modifications you like under the terms of the GPL:

http://www.gnu.org/licenses/old-license ... 0-faq.html

icaoberg wrote:2) this package requires Ice to be installed on the system. I've had problem installing Ice on Mac. I know about the posts in the forum and the website. But so far I've had no luck installing it on my Mac. Do you have a clue as to why? I've given up but I would like to know if you have an idea regarding this issue.

Mac OS X 10.6? You may have better luck with the pre-compiled Ice binaries available courtesy of Glencoe Software, Inc. outlined on the installation page:

http://www.openmicroscopy.org/site/supp ... stallation