Omero use world wide?

Dear Omero helpdesk,

I am perparing some slides about omero, and it would be a good idea to put some statistics about the use of omero world wide with, if possible, examples of big institutions…

We are willing set up the production launch by september, and such information could help a lot when presenting the project to all research teams.

best regards

Nabila Elarouci

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Hi Nabila-

Thanks for the information request. Due to GDPR and a general principle to respect our users privacy, we don’t directly track OMERO usage. OME software (i.e., Bio-Formats and OMERO) do perform upgrade checks, to provide sysadmins and users with reminders that new versions are available. We log the IP address and OS version for these upgrade checks. These checks use standard https protocols and thus are blocked by most institutional firewalls. Nonetheless, we detect ~3000 OMERO servers installed worldwide. Based on informal surveys, we estimate that about one-third of those are production systems. These numbers are on the scale of the number of life sciences research institutions worldwide, although we anecdotally know of OMERO installations outside of the life sciences sector.

A few examples of public OMERO and public resources that use/discuss OMERO.

  1. Image Data Resource– https://idr.openmicroscopy.org
  2. Systems Science of Biological Dynamics Database-- http://ssbd.qbic.riken.jp/
  3. Dundee Life Sciences data publication-- https://omero.lifesci.dundee.ac.uk/
  4. Liverpool OMERO Gallery https://cci02.liv.ac.uk/gallery/ (note an updated version of OMERO.gallery is upcoming)
  5. Queensland Brain Institute-- https://omerocloud.qbi.uq.edu.au
  6. EMPIAR SliceViewer (e.g., https://www.ebi.ac.uk/pdbe/emdb/3dbrowse/empiar_10055_l-schizont_2)
  7. Harvard Med School CycIF Data: https://omero.hms.harvard.edu
  8. OHSU LINCS Proiect Image Data: https://omero.lincsclarion.org
  9. HMS LINCS project Image Data: https://lincs-omero.hms.harvard.edu
  10. Example of institutions evaluating OMERO: https://speakerdeck.com/olatarkowska/towards-decentralized-lifescience-image-data-resources

Some of these are listed on https://www.openmicroscopy.org, but it’s time to review the list. If anyone else would like to have their OMERO instance linked , please let us know below.

Cheers,

Jason

3 Likes

Hi Jason,
Many thanks for these information. that could help me a lot in the presentation. French researchers like have a statistical view :slight_smile:
I will tell you in september if we accept to link our omero instance to you rlist.

best wishes

nabila

Hi Nabila

No problem at all. I think it’s probably not just French researchers who like numbers!!!

Good luck with the discussions. If you need anything else, just shout.

Cheers,

Jason

Hi Jason,
I like the OME picture in https://speakerdeck.com/olatarkowska/towards-decentralized-lifescience-image-data-resources?slide=4

I will use it (with reference to ome of course) to introdure the and illustrate the need of a data management tool like Omero.
have you any repository where can we find such figures, please?

with best regards

Nabila

Hi Nabila-

Great-- make sure to credit Aleksandra Tarkowska, Wellcome Sanger Centre.

A repository for example image data? For that, there is IDR (https://idr.openmicroscopy.org).

Or slides and figures? OME slides and presentations are posted at https://downloads.openmicroscopy.org/presentations/. [I have often thought that the open bioimaging projects should post current slides etc on F1000, Zenodo or somewhere where community can find them; just been a bit too busy to make that happen. Any volunteers?.]

Thanks again.

Cheers,

Jason

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Another external list of institutions with thanks to @sukunis :

currently (Nov. 2020) including:

  • Heinrich Heine University Duesseldorf
  • University of Osnabrueck
  • University of Muenster
  • University of Cologne
  • Saarland University
  • University of Duisburg-Essen