[ome-users] Nikon ND2 Time information
Kraft, Lewis James
lewis.j.kraft at Vanderbilt.Edu
Mon Jun 10 17:07:00 BST 2013
Hi Curtis,
Thanks for the helpful advice. I will account for this possibility in the future.
Melissa,
I would like to be notified automatically of any changes to the ticket.
Best,
Lewis
From: ctrueden.wisc at gmail.com [mailto:ctrueden.wisc at gmail.com] On Behalf Of Curtis Rueden
Sent: Friday, June 07, 2013 9:46 AM
To: Melissa Linkert
Cc: Kraft, Lewis James; OME-users ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Nikon ND2 Time information
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<mailto: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<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><mailto: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<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<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><mailto: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><mailto: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
>
>
>
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>
> 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
> _______________________________________________
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