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Workflow guide for importing images to OMERO.web

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There are workflow guides for various OMERO functions on our help site - http://help.openmicroscopy.org

You should find answers to any basic questions about using the clients there.

Workflow guide for importing images to OMERO.web

Postby maxgitt » Wed Nov 01, 2017 7:48 pm

The workflow guide http://help.openmicroscopy.org/web-client.html gives a basic example of how to view images in the web client, but as far as uploading goes, there is only a guide on how to upload files to OMERO.insight.

Is there a way to upload files to OMERO.web or am I restricted to OMERO.insight? And if so how? I can't seem to find any button or walkthrough on how to actually submit an image to OMERO.web.
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Re: Workflow guide for importing images to OMERO.web

Postby jmoore » Wed Nov 01, 2017 8:08 pm

Max,

there's currently no way to import via OMERO.web. You'll want to use `bin/omero import` from within the docker image:

Code: Select all
$ docker run -ti --rm --entrypoint=python openmicroscopy/omero-server:5.4.0 /opt/omero/server/OMERO.server/bin/omero import -h


You'll want to mount the data into the container via --volume so it can be imported and to link in the server docker via --link so that you can access the server by name.

Cheers,
~Josh
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Re: Workflow guide for importing images to OMERO.web

Postby maxgitt » Wed Nov 01, 2017 8:30 pm

This doesn't seem like a viable solution for "non-technical" scientists. It appears OMERO.insight is currently under maintenance. Would this be your recommendation for allowing an easy to use UI?

I don't want my users to worry about using the commandline to upload microscopy data (most of them are Bioengineers or Biology researchers).
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Re: Workflow guide for importing images to OMERO.web

Postby jmoore » Wed Nov 01, 2017 9:42 pm

maxgitt wrote:This doesn't seem like a viable solution for "non-technical" scientists. It appears OMERO.insight is currently under maintenance. Would this be your recommendation for allowing an easy to use UI?


Insight is in maintenance mode, yes, meaning new features will not be added, but critical bugs will be fixed. For the moment, it is certainly the intended GUI workflow.

I don't want my users to worry about using the commandline to upload microscopy data (most of them are Bioengineers or Biology researchers).


Understood.
~Josh
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Re: Workflow guide for importing images to OMERO.web

Postby maxgitt » Thu Nov 02, 2017 3:40 pm

Thanks for the information. I'd hope there is a plan to increase functionality of OMERO.web to include the ability to upload files. This would seem an important feature for an imaging tool.
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Re: Workflow guide for importing images to OMERO.web

Postby jmoore » Thu Nov 02, 2017 3:49 pm

Definitely on the roadmap!
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