All data within OMERO Plus belongs to a particular Group, and Users are added as Group Members. Therefore, sharing data happens by adding relevant Users to a Group and/or adding data to a Group. Permissions are handled at the Group-level, rather than at the data-level. See here for a detailed description.
If a copy of the data should be shared (for example, for publication or with external collaborators), it is possible to duplicate OMERO data for sharing without duplicating the underlying image files.
Over 160 file formats are supported in OMERO Plus through Glencoe’s Bio-Formats library. The list of supported file formats can be found here.
Large images (> 3000 x 3000 pixels in X and Y) require resolution pyramids in OMERO Plus for optimal web visualization. Most modern file formats, even proprietary ones from the microscope vendors, support this, but there are some exceptions. Either check in with the microscope vendor or convert the image to an open standard file format like OME-TIFF or OME-Zarr using Glencoe’s open source NGFF-Converter, as pyramids are also generated during conversion. Once conversion is complete, re-import the data to see your thumbnails and load images in PathViewer.
This can happen if the range of pixel values in your image does not fill the full dynamic range of your data type, e.g. if the maximum pixel value in your image is 5,000 but your 16-bit data allows for values between 0 and 65,535. You can save more appropriate per-channel min and max values in the Preview tab in OMERO.web or under Viewing Options in PathViewer, which will then also update the thumbnail. Note these are settings for visualization only and are not modifying the underlying data.
By default, OMERO Plus users see the rendering settings set by the owner of the OMERO Image. Users can save their own rendering settings separate from the owner, and then their own rendering settings will be shown to them by default in the future. If multiple users have saved rendering settings, you will be able to see those under the Viewing Options in PathViewer and in the Preview tab in OMERO.web. From there, you can select the rendering setting of interest and save as your own or copy to another image.
Double check that your username and password have been entered correctly. Especially if you log in with institutional credentials (for example: SSO, LDAP, etc.), contact your internal administrator for any broader issues. They will also be able to confirm if you have an active user account, and check the status of the OMERO Plus services. They will help diagnose and contact our team for support.
This message is shown if the OMERO Plus web application is not running. Usually this is because we are upgrading your OMERO Plus instance. Please reach out to your OMERO Plus internal administrator first to confirm if any scheduled downtime was planned.
OMERO.server
The main application server portion of OMERO. This is responsible for a majority of the heavy lifting done from an image management standpoint. While deployed and treated as a single application the OMERO.server is a collection of processes that serve different functions. Those processes are enumerated below with their core language in parenthesis.
OMERO.web
The primary Python/Django web application that interacts with OMERO.server. OMERO.web is a specialized client of the OMERO.server and is not strictly required to use OMERO, however it’s the primary point of interface for most users as it provides visualization and other key functionality.
OMERO.ms
OMERO Plus utilizes a microservice architecture in order to offload certain functionality away from the OMERO.server to dedicated microservices. This is done primarily for performance but additionally for functionality.
Redis
Provides ephemeral session storage between django and the microservices.
PostgreSQL
Metadata storage. Note: No binary data is stored in PostgreSQL.
NGINX
SSL termination, serves static files (UI elements, etc), acts as an endpoint router for microservices.
File Locations
Logs
When issues arise in OMERO Plus, you will often be asked to send log files for investigation. Log files are stored in the following locations:
You will find the latest information on our most recent release on our blog which typically includes a new release of: Glencoe’s Bio-Formats, PathViewer and OMERO Plus.
Check here to see if you have the latest OMERO.server version. The versions of your own installation can be found in the web interface under <hostname>/feedback/comment. If you would like to upgrade, please do not hesitate to contact our team at support@glencoesoftware.com who will assist in scheduling this.
