[ome-users] Bio-Formats Import OME-XML metadata timestamp problem since 5.2.0

[George Patterson]

Hi all,
After a recent FIJI update, we have encountered a problem with the metadata
from our experiments using Micromanager.  In these experiments, we collect
three channel data, but for two channels the images are collected only
every 10th time point.  We've been running these type of experiments for
some time now and only recently found that the timestamps do not match the
image times.  If we display the OME-XML metadata when importing using
Bio-Formats and look at the Plane information located at the bottom, the
metadata shows all three channels taken sequentially for the whole
experiment.   Because the two skipped channels are listed as if imaged at
every time point, the DeltaT values are correlated with the wrong channels.

I can reproduce this with a small data set collected using the demo mode of
Micromanager.  I'll upload it to the QA system shortly.  For this example,
Channel 0 (1 sec exp), Channel 1(0.1 sec exp), and Channel 2 (0.01 sec exp)
are imaged, then Channels 0 and 1 are skipped for 9 time points.  This is
repeated for 3 cycles for a total of 3 images each of Channels 0 and 1 and
30 images of Channel 2.
My colleague has traced this change to occur with the release of
Bio-Formats 5.2.0.  I hesitate to refer to this as a bug since it looks
like numerous changes occurred between 5.1.10 and 5.2.0 and this could just
be a feature change that we are not using properly.
We did our tests of the different versions of Bio-Formats using ImageJ
1.51a, but as I mentioned earlier we initially discovered it using an
updated FIJI.
Computers used are a Mac Pro running 10.9.5 and Macbook Pro running 10.10.5.
My apologies if I missed the discussion of this issue on the listServs.  If
you could direct me there I'd appreciate it.
Thanks for any clarification if it's a feature and any help if it's a bug.
And as always, thanks to OME and Bio-Formats teams for sharing.
Best,
George
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