Open Microscopy Environment

Hi people,

I work in a group performing plenty of wide field fluorescence imaging (PALM, STORM, SOFI, ...). The amounts of data being generated are quite large and currently we are pretty much using external USB2.0 (USB3.0 if we are lucky) external drives to ferry data around.

This is of course totally inefficient. We need to be able to store/annotate/analyze/share data in a more robust way.

This is where OMERO could be useful but since we lack the ability or the desire to start running our own storage servers we were wondering if it would not be feasible to run OMERO on one of the many cloud platforms that are available today (Amazon S3, Microsoft Azure, Google Compute/Storage Cloud, ...). I think this would make more sense from a redundancy/cost perspective.

However, as I understand, OMERO server is not a full storage solution in itself. It still relies on a standar disk filesystem (correct me if I am wrong).

Although I am personally aware of the broad concepts involved in implementing solutions like these I lack the full insight to be able to assess how feasible it would be to undertake such an effort (i.e. host OMERO on a cloud platform).

Could any of you point me in the right direction? Who could I talk to, who could assist in setting up? Anyone with experience in this respect?

Cheers,

Kris

Hi Kris,

Thanks for showing interest in the OMERO platform. The software's design indeed requires a file system and a database to store the image files and metadata. More on that can be read here: http://www.openmicroscopy.org/site/supp ... index.html. An explanation what is stored on the file system in the binary repository is presented here: http://www.openmicroscopy.org/site/supp ... itory.html.

We have not explored the cloud infrastructure storage option yet. There is however the OVA image that would allow you to try OMERO: http://downloads.openmicroscopy.org/ome ... .2-b26.ova.

Regards,
Blazej

Is there any update on setting up OMERO on a cloud-based server (such as Amazon)?

Hi alamsa,

there's still no support for making use of block storage like S3 in OMERO 5.2. That being said, running OMERO in a hosted environment works well. Your primary consideration will have to be what form of (non-block) storage is sufficiently performant and affordable for you.

Regards,
~Josh