Open Microscopy Environment

Hi,

In order to allow for a simple form of integration with another record-keeping system we'd like to investigate whether the OMERO.webclient would be an option.

We are thinking about an 'integration' via a URL. Currently, you can refer with a link to any individual image.
This post https://www.ome-xml.org/community/viewtopic.php?f=6&t=634&sid=7f2396d796b59353a22b8211c5b2fdae seems related but I don't have enough insight into the options for displaying results in a web browser.
Would it technically be possible to link to datasets and projects in a web browser using an unique URL ?

Thanks a lot for your feeback.

Best,
Alexander

I would also be interested in doing this

Hi,

Yes, this is certainly possible.
(I don't think the forum link above is talking about what you want).

What sort of page do you want to link to?
This movie demonstrates the latest (4.3, just released) web client.
http://cvs.openmicroscopy.org.uk/snapsh ... UI-4.3.mov

You'll notice that when an image is selected at the start, the url has the project|dataset|image IDs. This allows you to link to specific points in the webclient - However, this functionality is quite new and still under development (E.g. can't link directly to dataset or image, project linking doesn't do selection AND expansion of tree - /webclient/userdata/?path=project=52:selected does selection).

Is this kind of functionality sufficient for your needs? Or do you need to link to something else?

If you want to do some development in the OmeroWeb framework, then "everything" is possible. Have a look at the introduction page https://trac.openmicroscopy.org.uk/ome/wiki/OmeroWeb and movie http://cvs.openmicroscopy.org.uk/snapsh ... ro-4.3.mov

Will.

Hi Will,

Thanks for your quick reply and the link to the movie.
The recent developments are close to what we thought about.

What we are aiming for would be something like:
In our documentation system, we would paste a link '.../webclient/userdata/?path=project=52:selected' into a dedicated field.
If you then would click on this link, a browser with OMERO.webclient would be launched and after login the user would be directed to the project.

I'll do some tests with the new webclient and my demo OMERO account. And anything else would be up to programming

Thanks,

Alexander

Dear Alexander

To clarify what is good practice in terms of landing page.
In 4.3.0 landing page concept were defined as:

Code: Select all

http://host:port/url/path=server=1|project=1|dataset=2|image=3:selected


where selected flag can be put on one of the data parameters (project, dataset, image) which populate metadata panel loading.

There is no authentication step and this link is for internal use only. This is prototype and you should not use it in the production context now. Future development will continue in http://trac.openmicroscopy.org.uk/ome/ticket/6103

That feature has been announced under omeroweb/webredirect application and future development will continue as stated. The url given by Will (.../webclient/userdata...) is the internal application link, where the proxy currently redirects to.

Thanks
Ola

Hi all,

At VIB, we are starting up an OMERO project and would like to work towards an integration between our electronic lab notebook system and the OMERO data.

Therefore, I was wondering whether there has been any progress on the mentioned features ('landing pages' http://trac.openmicroscopy.org.uk/ome/ticket/6103) or whether there have been requests from other OMERO users?


Thanks a lot for the feedback.

Best regards,
Alexander

Hi Alexander

Currently we are in the process of discussing timeline for release of 4.4 with respect to priorities. That shouldn't stop us to start gathering all of the wish lists about possible 'landing page' extensions.
Based on the prototype (described in ticket 6103) currently available in OMERO 4.3.3 and existing image link functionality available in web viewer could you please give some feedback? Could you briefly describe your thoughts and expectations about integration between electronic lab notebook system and the OMERO data?

Thanks
Ola

Hey Alexandra

We created a catalogue of all our images in a specific dataset (stretching it to project would be no issue) and we are looking to move the source to sourceforge in the next couple of weeks if that helps? Otherwise I can email you what we have.

Hi Manda,

is the code inside of the ome git or an external project? If it's in the ome git having it as a patch to the github project (https://github.com/openmicroscopy/openmicroscopy) would be optimal, but any way that works for you would be appreciated.

Thanks!
~Josh.

Hi all,

I'm terribly sorry but I did not see that there have been some answers on this topic... forgot to check the box.

Basically, we would be fine with having links to projects and datasets (screens, plates). For the individual images, this is already possible.

In the notebook, you would enter a URL to the dataset which is clickable. This URL (landing page) would direct you to the attached project or dataset
.e.g. https://omeroserver:port/url/path=server=1|project=1
if you click the link in ELN, a web browser will be launched, you login to OEMRO via the OMERO webclient and are redirected to the linked project or dataset.

Hope that I'm clear and again sorry for the very late reply.

Best,
Alex