Open Microscopy Environment

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.

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

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).

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

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.

Definitely on the roadmap!
~Josh