Open Microscopy Environment

Hello all,

We plan to implement OMERO server here at the Van Andel Research Institute for about 20-40 users. The recommended specs are pretty clear online, except when it comes to graphics cards. We have a server unit available that seems like it should have more than meet most needs but I cannot find any guidance about what kind of graphics acceleration it will need. We plan on running OMERO integrated with Huygens deconvolution and Matlab, possibly along with IMARIS. The combined 3D display and manipulation needs seem like they would ask for a lot of GPU juice.

Any help appreciated.

Tim Feinstein, Ph.D.
Van Andel Research Institute

Dear Tim,

Thanks for showing interest in the OMERO platform.
Regarding GPUs: there is no specific requirement for the server. The image is being rendered on the client computer. If you decide to use scripts within OMERO that require any specific graphic adapter capabilities (e.g. to speed up computed vision computations), then yes - it might make sense to have a fast GPU on the server.

With kind regards,
Blazej

Thanks for your reply. Maybe I should clarify my goals and see whether OMERO is suitable.

I want to centralize both data storage and analysis for the users of our facility. The main motivator is that a lot of analysis software is both expensive and demands a lot from the processor. The idea would be to have an OMERO server physically linked to a workstation running Huygens, Fiji and MATLAB linked to OMERO, along with other things like CellProfiler/Analyst, ilastik, Imaris (thanks to a former PI who bought a license, never used it and donated it to us) etc. I want to arrange it so that people can access their data directly with their OMERO client, but also access the workstation via e.g. remote desktop to run big tasks without melting their own CPU.

Do people do that? It seems like a tractable problem to me.

Do people do that? It seems like a tractable problem to me.

Hi Tim. I don't think anyone will have been able to reasonably do what you're describing with OMERO 4.4 and below since the stored data was quite opaque, e.g. an image would be spread across the files 6547, 6548, and 6549 or similar.

Starting with the upcoming OMERO 5 release, the ManagedRepository will be available for more user-friendly access. The primary intent, however, isn't really the use-case you're talking about, but we'd certainly be interested in hearing whether or not you can make it work for you.

Regards,
~Josh