[ome-devel] OME metadata in Micro-Manager

[Chris Weisiger]

Hello all,

In brief: Micro-Manager contains code for writing OME metadata, none of us
understand it, and it doesn't always work; help?

We at Micro-Manager recently discovered that we're using a badly
out-of-date version of the OME metadata libraries. I don't know exactly
what the version is, but it's still under the loci.common / loci.formats
namespace. This breaks our compatibility with Fiji (at least when it comes
to trying to save multipage TIFF files), which is pretty unfortunate.

Additionally, when bugs pop up, we're rather at sea. For example, I
recently discovered that we get an ArrayIndexOutOfBoundsException when
calling MetadataTools.populateMetadata() if the "series" parameter is not
provided "in order" (that is, if we hand it 1 first then it errors; if we
hand it 0 and then 1 then everything is fine). It took me a long time to
even figure that much out, because the error contained no explanation; I
had to compare the values of the arguments across multiple versions of
Micro-Manager and play "spot the difference".

Ideally, we'd patch our OME metadata-writing code so it could handle the
"unordered" case cleanly, but I'm not confident in my ability to change
this code without introducing potentially-subtle bugs. In fact, none of us
have any working knowledge of the OME library; apparently our
implementation was written for us by Melissa Linkert.

Micro-Manager doesn't actually read the OME metadata itself; it's present
solely so that other programs can load some of our metadata. We'd like to
upgrade our libraries to something more modern, but documentation appears
to be scarce, and I wouldn't really know where to get started. Any advice
would be appreciated.

Thanks for your time.

-Chris Weisiger
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