Testing a new service: OMERO

Welcome to the OMERO project page!

OMERO is your open-source platform for the professional management and analysis of image data in research, hosted at Goethe University in Frankfurt. Developed to meet the requirements of imaging sciences, OMERO enables the structured storage, management and sharing of large image datasets. The platform supports numerous file formats and allows for the central organisation of your data – including metadata, annotations and analysis results. Thanks to its high flexibility and expansion capabilities, OMERO can be seamlessly integrated into existing research infrastructures and promotes interdisciplinary collaboration within your team.

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Introduction of OMERO as a federated service

OMERO is currently planned to be offered as a central service for the GU Frankfurt, JGU Mainz and TU Darmstadt. There will be three project phases: the two test phases, Alpha and Beta, and the production phase – further details on the phases can be found below.

Access and costs

Access is planned to be available via the respective institutional accounts. Since OMERO will handle large volumes of data, it will be introduced as a paid service. The costs for storage will be passed on directly to users. As part of the project, storage requirements will be determined, and thus also the potential costs, which will be billed in € per TB per year.

Project phases

Testing the OMERO setup with selected user groups from the three RMU sites (GU, JGU, TUDa).

Installation of the open-source software OMERO at Goethe University.
Integration of a storage system for the test phases.
Integration of the SSO systems at the aforementioned sites.
Selection of test users and provision of access to OMERO.
Identification of further technical requirements in collaboration with the users.
Development and finalisation of a funding concept.
Development of a technical support model for the aforementioned locations.
Documentation of initial usage scenarios and workflows.
Please note: Data collected during the alpha phase will not be carried over to the beta phase.

Clarification of all organisational, legal and operational framework conditions.

Technical implementation of feedback from the alpha phase.
Implementation of automatic storage billing.
Establishment of a technical support service for the aforementioned locations.
Development and completion of data protection measures, privacy policy, terms of use, cooperation agreements and other necessary documents.
Provision of an OMERO instance with a new database.
Targeted onboarding with selected user groups.
System usage and performance monitoring begins.

Ongoing operation of OMERO as a centralized service at the RMU sites (GU Frankfurt, JGU Mainz, TU Darmstadt).

Regular onboarding of new user groups across the RMU sites.
Active promotion of the service within the academic community (e.g., via workshops, mailing lists, training sessions).
Ongoing operation and technical maintenance of the system.
Monitoring and scaling of storage and server capacities based on usage.
Coordination between the sites to further develop governance structures and ensure sustainable funding.
Maintenance and expansion of technical and legal documentation.
Long-term strategic development of the service within the context of the RMU.

FAQ

1. Core features and how to use them

How do I upload images/data sets to OMERO?

To upload images or datasets to OMERO, you need OMERO.insight: Click here to download. Launch the programme and enter the server address of our OMERO instance, which you will receive from our support team. To do this, click on the tool icon, then on the blue plus sign, enter the address and confirm with “OK” and “Apply”. Then log in with your OMERO account. You can then create folders and upload images or datasets using the “Import” function.

2. OMERO group permissions. This setting applies to the entire group/team.

Private (rw----)

All data in this group is visible only to its owner and the group owner. Other users cannot see who is in the group or view its data. The group owner can view the data but cannot edit it.

Read-only (rwr---)

Users can view other group members’ data, but cannot edit or comment on it. Other users’ images can be viewed, but not rated or tagged.

Read & Annotate (rwra--)

Users can view and annotate other members’ data: tag images, add comments and save their own display settings. The names of other users’ images, projects, records or tags must not be changed.

Read & Write (rwrw--)

Users can view, edit and delete other members' data.