[ome-devel] OMERO developments in Montpellier

Tue Sep 9 11:08:42 BST 2014

Dear Jean-Marie,

I see. So maybe integrating these functionalities into the current java importer app is not a good idea for the long run.

Would it be something to develop a GUI (in python for example) to create scripts that would run the python command line importer in the background. Maybe a quick and dirty solution? I don’t know.

For the tagging option on import, my idea was to have, on the options tab of the importer, in stead of the common tag adding tool, a window very much like the Douglas’ auto tagging tool. It is great and the few people that we showed to loved it. This would be anyway not a priority. Just an idea.

What is more pressing for us is to decide on a solution for the off-line import.

What would be also important is manage, a link to the raw files on disk. We use a lot imaris. Douglas was mentioning something like a tool on the web browser or client that, when clicked, you would get a link (ideally automatically redirected) to the file on a mounted disk. That would be great.

Best, Julio

On 03 Sep 2014, at 17:54, Jean-Marie Burel <j.burel at dundee.ac.uk> wrote:

> 
> Dear Julio
> Great news to hear that you are adopting OMERO at RIO.
> Having an "off-line import" is certainly a feature that will be useful to other sites since many institutes have a similar model to run their facility (hour fee)
> 
> As you probably already know, the development of the Java client started several years ago.
> We made technical decisions at the time based on what was available and if not available we had to write our own libraries, e.g. event bus library, concurrency library. So some sections of the code are in serious need of modernisation.
> We are now exploring new avenues so we can take advantage of more modern technologies and also increase our client development velocity. We have not yet planned  any development. This depends on several factors.
> In the meantime:
> we are adding key missing functionalities to both Java and Web clients e.g. Search, work on viewer, etc.
> We are extracting components out of the current Java client code base e.g. Work on the Java Gateway see https://github.com/openmicroscopy/openmicroscopy/pull/2363 so it is accessible to other Java clients. Feedback on what is needed will be much appreciate.
> For the tagging tool, 
> Are you thinking to enforce tagging at import time? How do you see it  fit with your "off-line" import? Will it not be more suitable to write scripts with some of the concept of Douglas's tagging tool, scripts that you run post-import and if the images  for example do not have the required metadata, the user is notified.
> 
> Cheers
> Jmarie
> 
> 
> 
> From: Julio Mateos Langerak <Julio.Mateos-Langerak at igh.cnrs.fr>
> Date: Tuesday, 2 September 2014 09:27
> To: OME Development <ome-devel at lists.openmicroscopy.org.uk>
> Subject: [ome-devel] OMERO developments in Montpellier
> 
> Dear all,
> 
> After a nice summer I’m posting for the first time in this list. Hope you also enjoyed the summer.
> 
> As some of you might know, at Montpellier RIO Imaging, we are going to adopt OMERO. We are interested in developing onto the OMERO platform and adapt some of the tools to meet some of our needs. We believe these developments will be very useful for the rest of the user community, mainly in the context of big core facilities. To give you an idea, we have some 700 users and 60 acquisition stations. For this we are planing to hire a developer for an initial period of 1 year (we have the financing for this already).
> 
> We are now going through the process of defining our priorities, seing which things are already done, being done or tried by others, etc etc… So any feedback is very very welcome. Also, we have to write a profile for the developer and that will depend to some extent on what we want to do.
> 
> What we really need is an "Off-line import”. The idea is to give the option, probably in the form of a second import button called something like “import off-line”. This will launch the import routine and the user can logoff the machine and the import will happen in the background without using too many resources. The advantage being that a next user can access the machine without his acquisition being disturbed by the import process. Also, as our facility works on a per hour fee, this will also benefit the users.
> 
> A second thing could be a better tagging tool in the importer. Maybe adopting the concept of Douglas in the auto-tagger.
> 
> Our initial idea is to work on the current java client and adapt it with to man features. What is you opinion on this?
> 
> Best, Julio
> 
> 
> 
> __________________________________________
> Julio Mateos Langerak, PhD.
> OMX manager
> Arnaud de Villeneuve Campus Imaging Facility
> Montpellier RIO Imaging
> Montpellier BIOCAMPUS, UMS3426
> Institut de Génétique Humaine-CNRS
> 141, rue de la Cardonille
> F-34396 Montpellier (France)
> e-mail: Julio.Mateos-Langerak at igh.cnrs.fr
> phone: +33.4.34.35.99.90
> fax: +33.4.34.35.99.01
> URL: http://www.mri.cnrs.fr/
> __________________________________________
> 
> 
> 
> 
> 
> 
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096

__________________________________________
Julio Mateos Langerak, PhD.
OMX manager
Arnaud de Villeneuve Campus Imaging Facility
Montpellier RIO Imaging
Montpellier BIOCAMPUS, UMS3426
Institut de Génétique Humaine-CNRS
141, rue de la Cardonille
F-34396 Montpellier (France)
e-mail: Julio.Mateos-Langerak at igh.cnrs.frphone: +33.4.34.35.99.90
fax: +33.4.34.35.99.01
URL: http://www.mri.cnrs.fr/
__________________________________________

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