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Import under OMERO.fs

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This documentation is for the new OMERO 5.3 version. See the latest OMERO 5.2.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.


OMERO.fs is a series of on-going changes designed to improve the way an OMERO.server interacts with existing directories of acquired image data. It currently consists of two components:

OMERO.dropbox is designed for watching a directory and kicking off an automatic import. The configuration of the DropBox system is covered on the OMERO.dropbox system administrator’s page.

OMERO.fs Managed Repository is designed to store original data in an unaltered form without requiring the data duplication that was carried out by a pre-5.0 import. The changes to the import system mean that an OMERO.fs server stores the original files in the ManagedRepository, preserving file names and any nested directory structure. The repository may even contain direct in-place links to original data without an file upload step. These changes improve the way OMERO deals with High Content Screening (HCS) and other complex heterogeneous data types, reducing storage requirements and using Bio-Formats to recognize Filesets (groups of files which correspond to multi-dimensional images and accompanying information) so they can be treated as single entities within the OMERO clients. OMERO.fs has some configuration properties that allow sysadmins to customize it for their site; developers should be aware of the how the new import process works and how this is affected by the configuration.