[ome-users] OME & Micro-Manager: metadata matters

[Sebastien Besson (Staff)]

Dear everyone,

following recent threads posted both on the OME mailing list [1] and on the Micro-Manager
mailing list [2],  we have updated Bio-Formats to support parsing  of Micro-Manager metadata stored in JSON format [3].

For users wanting to benefit from these improvements:
- if the data is saved as “Separate Image Files”, the metadata should be automatically read
- if the data is saved as “Image Stack Files”, then the “Create metadata.txt file with Image Stack Files” needs to be selected in the Tools > options menu. Clients using Bio-Formats (ImageJ/Fiji, OMERO, Icy…) should point at the metadata.txt file and not the .ome.tif. file(s) in order to parse the JSON metadata [4]

These additions have been released as part of Bio-Formats 5.1.8 and will be bundled with the next release of OMERO. Note that for data saved image file stack to load properly, both the OMERO server and the client used for importing data will need to be upgraded to 5.2.2.

Many thanks to Thomas Julou and Chris Weisiger for their input and the shared datasets [5].
Supporting custom metadata formats is important, but also challenging for us and the wider community.  A larger discussion about the utility of OME’s metadata tools, OME's response to continuing requests for updates and changes, and the best extension points for Micro-Manager and others, is clearly necessary. Note that our next proposal for Bio-Formats support and development aims to improve these extension points [6]. More Letters of Support are welcome!!!

Best,
The OME team

[1] http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-January/005825.html
[2] http://micro-manager.3463995.n2.nabble.com/Loading-MM2-datasets-with-bioformats-scifio-td7586511.html#a7586596
[3] https://micro-manager.org/wiki/Micro-Manager_File_Formats
[4] https://www.openmicroscopy.org/site/support/bio-formats5.1/formats/micro-manager.html
[5] http://downloads.openmicroscopy.org/images/Micro-Manager
[6] http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-February/005853.html

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