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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Curtis,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks for the helpful advice. I will account for this possibility in the future.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Melissa,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I would like to be notified automatically of any changes to the ticket.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Lewis<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> ctrueden.wisc@gmail.com [mailto:ctrueden.wisc@gmail.com]
<b>On Behalf Of </b>Curtis Rueden<br>
<b>Sent:</b> Friday, June 07, 2013 9:46 AM<br>
<b>To:</b> Melissa Linkert<br>
<b>Cc:</b> Kraft, Lewis James; OME-users ome-users@lists.openmicroscopy.org.uk<br>
<b>Subject:</b> Re: [ome-users] Nikon ND2 Time information<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">Hi everyone,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">One quick word of caution to Lewis and anyone else using the omeMeta.getPlane* methods.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">> <span style="font-size:10.0pt;font-family:"Arial","sans-serif"">deltaT = double(omeMeta.getPlaneDeltaT(iSeries, iPlane));</span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">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:<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"> omeMeta.getPlaneTheZ(iSeries, iPlane);<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"> omeMeta.getPlaneTheC(iSeries, iPlane));<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"> omeMeta.getPlaneTheT(iSeries, iPlane);<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">> java.lang.IndexOutOfBoundsException: Index: 0, Size: 0<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">The IndexOutOfBoundsException happens if there is no Plane #iPlane in the metadata. You can determine that in advance using:<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"> omeMeta.getPlaneCount(iSeries);<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">There is a complete example of how to extract planar timings at:<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"> <a href="https://github.com/openmicroscopy/bioformats/blob/v4.4.8/components/bio-formats/utils/PrintTimestamps.java" target="_blank">
https://github.com/openmicroscopy/bioformats/blob/v4.4.8/components/bio-formats/utils/PrintTimestamps.java</a><o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">It is in Java but the calls from MATLAB are analogous.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">Regards,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">Curtis<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">
<o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">On Fri, Jun 7, 2013 at 9:29 AM, Melissa Linkert <<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>> wrote:<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">Hi Lewis,<br>
<br>
There is now a ticket on our issue tracking system to fix timestamp<br>
population for FV1000 .oib and .oif files:<br>
<br>
<a href="http://trac.openmicroscopy.org.uk/ome/ticket/11087" target="_blank">http://trac.openmicroscopy.org.uk/ome/ticket/11087</a><br>
<br>
If you would like to be automatically notified of changes to that<br>
ticket, please let us know and we will CC you.<br>
<br>
Regards,<br>
-Melissa<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><br>
On Fri, Jun 07, 2013 at 02:05:45PM +0000, Sebastien Besson wrote:<br>
> Dear Lewis,<br>
><br>
> 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.<br>
><br>
> In general, copying the ome-users mailing list is recommended as it is likely other users will have similar questions/requests.<br>
><br>
> Best,<br>
> Sebastien<br>
><br>
> On 7 Jun 2013, at 13:43, Kraft, Lewis James wrote:<br>
><br>
> Thanks for your reply Sebastien. I really love the idea of this Bio-Formats project.<br>
><o:p></o:p></p>
</div>
<p class="MsoNormal" style="margin-left:.5in">> 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<<a href="http://qa.openmicroscopy.org.uk/qa/feedback/7327/?token=3b2871d8289d90282cd70f95807e4c37" target="_blank">http://qa.openmicroscopy.org.uk/qa/feedback/7327/?token=3b2871d8289d90282cd70f95807e4c37</a>>).<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">><br>
> 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?<br>
><br>
> 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.<br>
><br>
> Best,<br>
> Lewis<br>
><br>
> From: Sebastien Besson [mailto:<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>]<br>
> Sent: Friday, June 07, 2013 4:42 AM<br>
> To: Kraft, Lewis James<o:p></o:p></p>
</div>
<p class="MsoNormal" style="margin-left:.5in">> Cc: OME-users <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">
ome-users@lists.openmicroscopy.org.uk</a><mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>><o:p></o:p></p>
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<div>
<p class="MsoNormal" style="margin-left:.5in">> Subject: Re: [ome-users] Nikon ND2 Time information<br>
><br>
> Hi Lewis,<br>
><br>
> first of all, I am forwarding this conversation to the ome-users mailing list.<br>
><br>
> Regarding your email, there is no PlaneDeltatT field for the .oib format as listed in
<a href="http://www.openmicroscopy.org/site/support/bio-formats4/formats/olympus-fluoview-fv1000-metadata.html" target="_blank">
http://www.openmicroscopy.org/site/support/bio-formats4/formats/olympus-fluoview-fv1000-metadata.html</a>.<br>
> Thus the error below is not informative but expected.<br>
><br>
> As shown in the metadata table above, you should be able to read the PixelsTimeIncrement instead, i.e. for the first image series:<br>
> timeIncrement = double(omeMeta.getPixelsTimeIncrement(0));<br>
><br>
> Hope this helps,<br>
> Sebastien<br>
><br>
> On 6 Jun 2013, at 22:51, Kraft, Lewis James wrote:<br>
><br>
><br>
> Dear Sebastien,<br>
><br>
> Today I tried to read an Olympus .oib file. I received the following error which I traced back to the following line of code:<br>
><br>
> time(index1)=double(omeMeta.getPlaneDeltaT(0,index1-1));<br>
><br>
> Java exception occurred:<br>
> java.lang.IndexOutOfBoundsException: Index: 0, Size: 0<br>
><br>
> at java.util.ArrayList.RangeCheck(Unknown Source)<br>
><br>
> at java.util.ArrayList.get(Unknown Source)<br>
><br>
> at ome.xml.model.Pixels.getPlane(Pixels.java:600)<br>
><br>
> at loci.formats.ome.OMEXMLMetadataImpl.getPlaneDeltaT(OMEXMLMetadataImpl.java:3631)<br>
><br>
> Do you have any ideas on what might have gone wrong?<br>
><br>
> Thanks much,<br>
> Lewis<br>
><br>
> From: Kraft, Lewis James<br>
> Sent: Friday, May 31, 2013 4:42 PM<br>
> To: 'Sebastien Besson'<br>
> Subject: RE: [ome-users] Nikon ND2 Time information<br>
><br>
> Dear Sebastien,<br>
><br>
> Ah Ha! You are exactly correct! Many thanks!<br>
><br>
> Cheers,<br>
> Lewis<br>
><br>
> From: Sebastien Besson [mailto:<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>]<br>
> Sent: Friday, May 31, 2013 4:41 PM<br>
> To: Kraft, Lewis James<br>
> Subject: Re: [ome-users] Nikon ND2 Time information<br>
><br>
> Hi Lewis,<br>
><br>
> This is because the series and the plane index are 0-based. So to retrieve the first plane of the first series, try<br>
> deltaT = double(omeMeta.getPlaneDeltaT(0,0))<br>
><br>
> Cheers,<br>
> Sebastien<br>
><br>
> On 31 May 2013, at 22:33, Kraft, Lewis James wrote:<br>
><br>
> Thanks for the replies! Forgive me, for I am a bit clueless about the Java part of the programming, I tried the following:<br>
><br>
> >> deltaT = double(omeMeta.getPlaneDeltaT(1,1))<br>
> Java exception occurred:<br>
> java.lang.IndexOutOfBoundsException: Index: 1, Size: 1<br>
><br>
> at java.util.ArrayList.RangeCheck(Unknown Source)<br>
><br>
> at java.util.ArrayList.get(Unknown Source)<br>
><br>
> at ome.xml.model.OME.getImage(OME.java:600)<br>
><br>
> at loci.formats.ome.OMEXMLMetadataImpl.getPlaneDeltaT(OMEXMLMetadataImpl.java:3631)<br>
><br>
> 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?<br>
><br>
> Best,<br>
> Lewis Kraft<br>
><br>
> From: Sebastien Besson [mailto:<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>]<br>
> Sent: Friday, May 31, 2013 2:56 PM<br>
> To: Curtis Rueden<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal" style="margin-left:.5in">> Cc: Kraft, Lewis James; <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">
ome-users@lists.openmicroscopy.org.uk</a><mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>><o:p></o:p></p>
<div>
<p class="MsoNormal" style="margin-left:.5in">> Subject: Re: [ome-users] Nikon ND2 Time information<br>
><br>
> Hi Lewis,<br>
><br>
> with your variable names, you should be able to use the following to extract the timestamp of the plane iPlane for the series iSeries:<br>
><br>
> deltaT = double(omeMeta.getPlaneDeltaT(iSeries, iPlane));<br>
><br>
> As Curtis said, if this call leads to an error, you can send a sample file.<br>
><br>
> Regards,<br>
> Sebastien<br>
><br>
> On 31 May 2013, at 20:42, Curtis Rueden wrote:<br>
><br>
> Hi Lewis,<br>
><br>
> > Where can I find this time information for each image plane in the<br>
> > .nd2 files?<br>
><br>
> 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.<br>
><br>
> 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
<a href="http://qa.openmicroscopy.org.uk/qa/upload/" target="_blank">http://qa.openmicroscopy.org.uk/qa/upload/</a>), we can work on fixing the problem.<br>
><br>
> Regards,<br>
> Curtis<br>
><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in">> On Fri, May 31, 2013 at 2:35 PM, Kraft, Lewis James <<a href="mailto:lewis.j.kraft@vanderbilt.edu" target="_blank">lewis.j.kraft@vanderbilt.edu</a><mailto:<a href="mailto:lewis.j.kraft@vanderbilt.edu" target="_blank">lewis.j.kraft@vanderbilt.edu</a>>>
wrote:<br>
> Hello,<br>
><br>
><br>
> 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:<br>
><br>
> imgdata=bfopen(‘fullfilepath\*.nd2’); %command for opening images using BioFormats MATLAB scripts<br>
><br>
> img=imgdata{1,1}{1,1}; %First image in the timeseries<br>
><br>
> metadata=imgdata{1,2}; %Metadata in the .nd2 file<br>
><br>
> omeMeta = imgdata{1, 4}; %OME Metadata<br>
><br>
> 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?<br>
><br>
><br>
> Thanks much,<br>
> Lewis Kraft<br>
><br>
><br>
><br>
> _______________________________________________<br>
> ome-users mailing list<o:p></o:p></p>
</div>
<p class="MsoNormal" style="margin-left:.5in">> <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">
ome-users@lists.openmicroscopy.org.uk</a><mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>><o:p></o:p></p>
<div>
<p class="MsoNormal" style="margin-left:.5in">> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
><br>
> _______________________________________________<br>
> ome-users mailing list<o:p></o:p></p>
</div>
<p class="MsoNormal" style="margin-left:.5in">> <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">
ome-users@lists.openmicroscopy.org.uk</a><mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>><o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="margin-left:.5in">> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
><br>
> Dr Sébastien Besson<br>
> Open Microscopy Environment / Harvard Medical School<br>
> Wellcome Trust Centre for Gene Regulation and Expression,<br>
> College of Life Sciences, University of Dundee, Dow Street,<br>
> Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
><br>
><br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
><br>
> Dr Sébastien Besson<br>
> Open Microscopy Environment / Harvard Medical School<br>
> Wellcome Trust Centre for Gene Regulation and Expression,<br>
> College of Life Sciences, University of Dundee, Dow Street,<br>
> Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
><br>
><br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
><br>
> Dr Sébastien Besson<br>
> Open Microscopy Environment / Harvard Medical School<br>
> Wellcome Trust Centre for Gene Regulation and Expression,<br>
> College of Life Sciences, University of Dundee, Dow Street,<br>
> Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
><br>
><br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
><br>
> Dr Sébastien Besson<br>
> Open Microscopy Environment / Harvard Medical School<br>
> Wellcome Trust Centre for Gene Regulation and Expression,<br>
> College of Life Sciences, University of Dundee, Dow Street,<br>
> Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
><br>
><br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
<br>
> _______________________________________________<br>
> ome-users mailing list<br>
> <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br>
> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br>
_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><o:p></o:p></p>
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