[ome-devel] OMERO 5.3: Changing the way OMERO handles Plate and Image names on Import

[Jean-Marie Burel (Staff)]

Dear All


For the release of OMERO 5.3.0,

we are intending to change the way Image and Plate name are handled in the importer.


Currently, when images and plates are imported into OMERO 5.0.0+, unless a name is explicitly chosen, names are set by default to the filename identified by Bio-Formats and any name metadata is ignored. For images that are part of a multi-image fileset (MIF), the series number is used as part of the name in addition to the filename in order to distinguish between individual images.


The reason we are changing it is that  in order to preserve plate and image names encoded within metadata, users are required to perform their own metadata extraction. When importing a large number of plates, this effectively means that users must write scripts in order to import their data correctly, making them do the work Bio-Formats could be handling for them. This is also an issue for images, for example in digital pathology, where each image might have a self-describing name which is effectively lost on import with the current behaviour.


In OMERO 5.3.0, we propose to use name metadata provided by Bio-Formats unless the user has specifically overridden it or it isn't available, in which case it returns to the current behaviour.


In practice, this means that if you have developed an import workflow based on the current behaviour, you will need to adjust it. However, from 5.3.0, OMERO will respect your name metadata and hopefully simplify import for plates and multi-image filesets going forward.


For more details about tickets, code changes etc. please have a look at

https://github.com/openmicroscopy/design/issues/57



Thanks


The OME team

The University of Dundee is a registered Scottish Charity, No: SC015096
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