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

[George Patterson]

Dear Sebastien,
Thanks for the quick response and fix.
And again thanks for sharing your software with the rest of us.
Best,
George

On Thu, Oct 13, 2016 at 10:43 AM, Sebastien Besson (Staff) <
s.besson at dundee.ac.uk> wrote:

> Dear George,
>
> thank you very much for bringing this issue to our attention. We were able
> to reproduce the problem using the test data you uploaded.
>
> This change has been introduced as part of a 5.2.0 PR [1] and was aiming
> at reading and importing invalid OME-TIFF data. It turns out the
> assumptions upon which these modifications were relying  have undesired
> effects for valid OME-TIFF.
>
> As this constitutes a regression from a previously functional behavior, we
> will be working on a fix imminently and hope to release a Bio-Formats 5.2.4
> next week to address the problem.
>
> Best regards,
> Sebastien
>
> [1] https://github.com/openmicroscopy/bioformats/pull/2343
> [2] https://trello.com/c/aTV56qEX/6-fix-ome-tiff-regression-
> plane-population
>
> On 12 Oct 2016, at 21:23, George Patterson <geopascway at gmail.com> wrote:
>
> 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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