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What’s new for OMERO 5

OMERO 5.0 introduces the OMERO.fs (file system) changes needed to stop data duplication on import. Files are now imported and stored in their original format, preserving file names and directory structures, and reducing storage requirements. These changes, coupled with updates to Bio-Formats and the clients, improve the way OMERO handles complex multidimensional datasets.

  • Omero logging and Properties have been updated to explain the new logging configuration in OMERO.fs.
  • Deleting in OMERO has been updated to explain how OMERO 5 handles deleting multi-file images and image sets and to clarify the finality of deletion.
  • OMERO.fs has been updated to give an overview of the OMERO.fs project, and further details of the FS Managed Repository are being added.
  • OMERO.web has been upgraded to Django 1.6, requiring Python 2.6.5 or later. This enables more flexibility for developing new web apps and plugins. All the OMERO.web documentation has been updated to reflect these changes.
  • Introduction to OMERO.scripts and MATLAB and Python have been updated to reflect that MATLAB and Jython scripts are now supported natively.
  • Guidance for getting more involved with OME, and contributing to both OMERO and Bio-Formats, has been moved to our new Contributing Developer Documentation section so it is easier to find. It has also been updated to better explain our development processes.
  • OMERO Python language bindings describes additions to the BlitzGateway API to support Filesets.

Breaking changes

Breaking changes to the OMERO model and API were intentionally kept to a minimum. New methods and fields were added which you may want to make use of in your clients. There was, however, one breaking change.

The definition of one of the OriginalFile model object properties has changed: sha1 which used to contain the SHA1 hash (or checksum) of the file is now two properties: hash for the hash of the file, and hasher, an enumeration of type omero.model.ChecksumAlgorithm that describes which algorithm was used, for instance SHA1-160. When is called on a file with hasher set, it will set the file’s hash property to the correct value.

See the FS documentation for more information.