[ome-users] Bio-formats issue reading metadata from Micromanager files with nested summary elements

[Colin Fuller]

Hi--

I have a micromanager image whose metadata.txt file has a Summary element
nested within each FrameKey element within curly braces.  It appears that
any metadata in each FrameKey element that occurs after the nested Summary
element is not being read.  (For instance, this is where the camera gain
value occurs in my file, so if I use the bio-formats opener in FIJI and
show OME-XML metadata, the gain is listed as 0 rather than the actual
value.)

I'm using bio-formats updated to the trunk build through FIJI as well as a
build from source from the current develop branch on github, on linux with
openJDK 1.7.

I've attached a patch (from git-format-patch) for the micromanager reader
that fixes this issue for my images.  I'm happy to supply example images if
this would be helpful.

Thanks,

Colin Fuller
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