[ome-devel] Proposed tweak to µManager data files in 2.0

Chris Weisiger cweisiger at msg.ucsf.edu
Wed Apr 13 18:26:55 BST 2016

Hello all,

After discussion with some of our users and with the OME developers, I'm
creating this thread to invite comments on a proposed minor change to
µManager's "image stack file" storage format, in µManager 2.0 only (1.4
would not be changed). The "image stack file" format (which is the default
format) stores multiple image planes in the same TIFF file. This change
would be to the situation where multiple of these multi-plane TIFF files
are generated in a single dataset.

µManager writes multiple TIFF files in two situations: first, if there is
more than 4GB of data to store (as our TIFFs don't yet support BigTIFF),
and second, if the user has elected to store data for each stage position
in a separate file. Currently, the OME XML is written to a single one of
these files, and the other files are "pointed" to that file so they know
where to look to load the data in the XML. Thus in order to load any file
in the dataset, you must have not only that file, but also the TIFF file
that contains the OME XML.

The proposal is to instead write the XML to a newly-created file
(tentatively named "OMEXMLMetadata.companion.ome") that would exist in the
same directory as the TIFF files, display settings, comments, and
metadata.txt, as appropriate. As before, the TIFF files would be "pointed"
to this file; it would need to be present to use the BioFormats Importer or
any other OME library loader.

In situations where there is only one TIFF file, the OME XML would still be
stored in that TIFF file; the "OMEXMLMetadata.companion.ome" file would not
be generated. For reference, the XML would look something like this:


I've tested this change locally and haven't detected any problems, but I'm
not familiar with the kinds of workflows that our users may want to
perform, so any comments are welcome. Thanks for your time.

-Chris Weisiger and the µManager dev team
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