[ome-users] Nikon ND2 Time information
Curtis Rueden
ctrueden at wisc.edu
Fri Jun 7 15:46:06 BST 2013
Hi everyone,
One quick word of caution to Lewis and anyone else using the
omeMeta.getPlane* methods.
> deltaT = double(omeMeta.getPlaneDeltaT(iSeries, iPlane));
The above call gets the DeltaT for Image #iSeries, Plane #iPlane. However,
there is no explicit guarantee that that value corresponds to any
particular (Z, C, T) coordinate triple. But you can check what the (Z, C,
T) coordinates are for a given plane number using:
omeMeta.getPlaneTheZ(iSeries, iPlane);
omeMeta.getPlaneTheC(iSeries, iPlane));
omeMeta.getPlaneTheT(iSeries, iPlane);
> java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
The IndexOutOfBoundsException happens if there is no Plane #iPlane in the
metadata. You can determine that in advance using:
omeMeta.getPlaneCount(iSeries);
There is a complete example of how to extract planar timings at:
https://github.com/openmicroscopy/bioformats/blob/v4.4.8/components/bio-formats/utils/PrintTimestamps.java
It is in Java but the calls from MATLAB are analogous.
Regards,
Curtis
On Fri, Jun 7, 2013 at 9:29 AM, Melissa Linkert <melissa at glencoesoftware.com
> wrote:
> Hi Lewis,
>
> There is now a ticket on our issue tracking system to fix timestamp
> population for FV1000 .oib and .oif files:
>
> http://trac.openmicroscopy.org.uk/ome/ticket/11087
>
> If you would like to be automatically notified of changes to that
> ticket, please let us know and we will CC you.
>
> Regards,
> -Melissa
>
> On Fri, Jun 07, 2013 at 02:05:45PM +0000, Sebastien Besson wrote:
> > Dear Lewis,
> >
> > thanks for uploading your raw data. We will take a look at it and check
> if timestamps are present in the file that could be read by Bio-Formats.
> >
> > In general, copying the ome-users mailing list is recommended as it is
> likely other users will have similar questions/requests.
> >
> > Best,
> > Sebastien
> >
> > On 7 Jun 2013, at 13:43, Kraft, Lewis James wrote:
> >
> > Thanks for your reply Sebastien. I really love the idea of this
> Bio-Formats project.
> >
> > Is there any hope of having the Plane – DeltaT metadata field added for
> the .oib files? It would be nice to have at least this feature working for
> the file formats from the big 4 microscopes. I uploaded some test data for
> the Bio-Formats project (ID: 7327<
> http://qa.openmicroscopy.org.uk/qa/feedback/7327/?token=3b2871d8289d90282cd70f95807e4c37
> >).
> >
> > Unfortunately, I am a complete beginner when it comes to Java
> programming, and the details of the existing project, or I would offer my
> help adding the needed code. Perhaps there is an easier coding task that I
> might try to get my hands dirty with at first?
> >
> > Also, please forgive me if I am flooding the ome-user mailing list with
> this message - I am not familiar with what to post, and what not to post.
> >
> > Best,
> > Lewis
> >
> > From: Sebastien Besson [mailto:s.besson at dundee.ac.uk]
> > Sent: Friday, June 07, 2013 4:42 AM
> > To: Kraft, Lewis James
> > Cc: OME-users ome-users at lists.openmicroscopy.org.uk<mailto:
> ome-users at lists.openmicroscopy.org.uk>
> > Subject: Re: [ome-users] Nikon ND2 Time information
> >
> > Hi Lewis,
> >
> > first of all, I am forwarding this conversation to the ome-users mailing
> list.
> >
> > Regarding your email, there is no PlaneDeltatT field for the .oib format
> as listed in
> http://www.openmicroscopy.org/site/support/bio-formats4/formats/olympus-fluoview-fv1000-metadata.html
> .
> > Thus the error below is not informative but expected.
> >
> > As shown in the metadata table above, you should be able to read the
> PixelsTimeIncrement instead, i.e. for the first image series:
> > timeIncrement = double(omeMeta.getPixelsTimeIncrement(0));
> >
> > Hope this helps,
> > Sebastien
> >
> > On 6 Jun 2013, at 22:51, Kraft, Lewis James wrote:
> >
> >
> > Dear Sebastien,
> >
> > Today I tried to read an Olympus .oib file. I received the following
> error which I traced back to the following line of code:
> >
> > time(index1)=double(omeMeta.getPlaneDeltaT(0,index1-1));
> >
> > Java exception occurred:
> > java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
> >
> > at java.util.ArrayList.RangeCheck(Unknown Source)
> >
> > at java.util.ArrayList.get(Unknown Source)
> >
> > at ome.xml.model.Pixels.getPlane(Pixels.java:600)
> >
> > at
> loci.formats.ome.OMEXMLMetadataImpl.getPlaneDeltaT(OMEXMLMetadataImpl.java:3631)
> >
> > Do you have any ideas on what might have gone wrong?
> >
> > Thanks much,
> > Lewis
> >
> > From: Kraft, Lewis James
> > Sent: Friday, May 31, 2013 4:42 PM
> > To: 'Sebastien Besson'
> > Subject: RE: [ome-users] Nikon ND2 Time information
> >
> > Dear Sebastien,
> >
> > Ah Ha! You are exactly correct! Many thanks!
> >
> > Cheers,
> > Lewis
> >
> > From: Sebastien Besson [mailto:s.besson at dundee.ac.uk]
> > Sent: Friday, May 31, 2013 4:41 PM
> > To: Kraft, Lewis James
> > Subject: Re: [ome-users] Nikon ND2 Time information
> >
> > Hi Lewis,
> >
> > This is because the series and the plane index are 0-based. So to
> retrieve the first plane of the first series, try
> > deltaT = double(omeMeta.getPlaneDeltaT(0,0))
> >
> > Cheers,
> > Sebastien
> >
> > On 31 May 2013, at 22:33, Kraft, Lewis James wrote:
> >
> > Thanks for the replies! Forgive me, for I am a bit clueless about the
> Java part of the programming, I tried the following:
> >
> > >> deltaT = double(omeMeta.getPlaneDeltaT(1,1))
> > Java exception occurred:
> > java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
> >
> > at java.util.ArrayList.RangeCheck(Unknown Source)
> >
> > at java.util.ArrayList.get(Unknown Source)
> >
> > at ome.xml.model.OME.getImage(OME.java:600)
> >
> > at
> loci.formats.ome.OMEXMLMetadataImpl.getPlaneDeltaT(OMEXMLMetadataImpl.java:3631)
> >
> > This resulted in the following error message from MATLAB. I am not sure
> if it is my lack of understanding of iSeries and iPlane in your example
> below?
> >
> > Best,
> > Lewis Kraft
> >
> > From: Sebastien Besson [mailto:s.besson at dundee.ac.uk]
> > Sent: Friday, May 31, 2013 2:56 PM
> > To: Curtis Rueden
> > Cc: Kraft, Lewis James; ome-users at lists.openmicroscopy.org.uk<mailto:
> ome-users at lists.openmicroscopy.org.uk>
> > Subject: Re: [ome-users] Nikon ND2 Time information
> >
> > Hi Lewis,
> >
> > with your variable names, you should be able to use the following to
> extract the timestamp of the plane iPlane for the series iSeries:
> >
> > deltaT = double(omeMeta.getPlaneDeltaT(iSeries, iPlane));
> >
> > As Curtis said, if this call leads to an error, you can send a sample
> file.
> >
> > Regards,
> > Sebastien
> >
> > On 31 May 2013, at 20:42, Curtis Rueden wrote:
> >
> > Hi Lewis,
> >
> > > Where can I find this time information for each image plane in the
> > > .nd2 files?
> >
> > It is best to extract the timestamp information from the OME metadata
> (specifically: OME > Image > Pixels > Plane > DeltaT), since it has been
> standardized to a format-agnostic structure. Then you won't have to worry
> about whether your file is .lsm or .nd2 or etc.
> >
> > If the information is not present in the OME metadata, then it means
> Bio-Formats is not parsing and standardizing that information properly. In
> that case, if you send us a sample file (via
> http://qa.openmicroscopy.org.uk/qa/upload/), we can work on fixing the
> problem.
> >
> > Regards,
> > Curtis
> >
> > On Fri, May 31, 2013 at 2:35 PM, Kraft, Lewis James <
> lewis.j.kraft at vanderbilt.edu<mailto:lewis.j.kraft at vanderbilt.edu>> wrote:
> > Hello,
> >
> >
> > I am want to read the Nikon .nd2 image file using loci_tools.jar for
> MATLAB. I have successfully imported the image data using loci_tools.jar
> with the following MATLAB commands:
> >
> > imgdata=bfopen(‘fullfilepath\*.nd2’); %command for opening images using
> BioFormats MATLAB scripts
> >
> > img=imgdata{1,1}{1,1}; %First image in the timeseries
> >
> > metadata=imgdata{1,2}; %Metadata in the .nd2 file
> >
> > omeMeta = imgdata{1, 4}; %OME Metadata
> >
> > The Image data, and the OME metadata look fine. However, the original
> metadata is missing the time information. For example, when opening Zeiss
> .lsm files, I see the time information in metadata as,
> “*TimeStamp*,*TimeStamp*,…”. Where can I find this time information for
> each image plane in the .nd2 files?
> >
> >
> > Thanks much,
> > Lewis Kraft
> >
> >
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk<mailto:
> ome-users at lists.openmicroscopy.org.uk>
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk<mailto:
> ome-users at lists.openmicroscopy.org.uk>
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> > 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
> >
> > 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
> >
> > 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
> >
> > 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
>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
> _______________________________________________
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>
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