[ome-users] Reading Time Interval of OME metadata of mvd2 file

[Melissa Linkert]

Hi Tri,

> Thanks for reporting this issue . According to the Bio-Formats 5.0.0 documentation at
> http://www.openmicroscopy.org/site/support/bio-formats5/formats/volocity-metadata.html
> the metadata fields you are looking for to are not yet supported by the Bio-Formats
> Volocity reader.
> 
> To help you further, it would be very much appreciated if you could upload on of your Volocity
> files to:
> http://qa.openmicroscopy.org.uk/qa/upload
> Additionally, if you could supply us the expected time intervals as well, that would be extremely

Thank you for uploading a sample dataset as requested by Sebastien.  We
are now reviewing a fix for this:

https://github.com/openmicroscopy/bioformats/pull/987

We expect this to be fixed in the 5.0.1 release of Bio-Formats.  At that
time, the time intervals can be retrieved using getPlaneDeltaT(0,
planeIndex) (where planeIndex is the image number starting from 0).

Regards,
-Melissa

On Thu, Mar 20, 2014 at 08:36:56PM +0000, Sebastien Besson wrote:
> Hi Tri,
> 
> Thanks for reporting this issue . According to the Bio-Formats 5.0.0 documentation at
> http://www.openmicroscopy.org/site/support/bio-formats5/formats/volocity-metadata.html
> the metadata fields you are looking for to are not yet supported by the Bio-Formats
> Volocity reader.
> 
> To help you further, it would be very much appreciated if you could upload on of your Volocity
> files to:
> http://qa.openmicroscopy.org.uk/qa/upload
> Additionally, if you could supply us the expected time intervals as well, that would be extremely
> helpful.
> 
> Best regards,
> Sebastien
> 
> On 20 Mar 2014, at 18:12, Tri Thanh Pham <t.pham at unibas.ch<mailto:t.pham at unibas.ch>> wrote:
> 
> Hi Sebastien,
> 
> I am quiet new to Bio-Formats in Matlab and I have a bit of a problem in extracting the time interval from the OME metadata when loading .mvd2 file into matlab. When I try to extract the time interval using the following command: TimeInterval= double(omeMeta.getPixelsTimeIncrement(0));
> 
> It return [ ]. I get the same result when I use double(omeMeta.getPlaneDeltaT(0,0)). Can you please suggest how can I extract the time interval from this mvd2 file. Note that when I use volocity software to load this mvd2 file, it gives the correct value, which mean that the metadata does contain the time interval.
> 
> Regards
> Tri
> 
> Dr. Tri Thanh Pham
> Postdoctoral Research Fellow
> Biozentrum, University of Basel
> Klingelbergstrasse 50 / 70
> 4056 Basel, Switzerland
> Phone: +41 61 267 14 83
> 
> Dr Sébastien Besson
> Open Microscopy Environment / Harvard Medical School
> Wellcome Trust Centre for Gene Regulation and Expression,
> College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
> 
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096

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