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Hi Lewis,
<div><br>
</div>
<div>first of all, I am forwarding this conversation to the ome-users mailing list.</div>
<div><br>
</div>
<div>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">http://www.openmicroscopy.org/site/support/bio-formats4/formats/olympus-fluoview-fv1000-metadata.html</a>.</div>
<div>Thus the error below is not informative but expected.</div>
<div><br>
</div>
<div>As shown in the metadata table above, you should be able to read the PixelsTimeIncrement instead, i.e. for the first image series:</div>
<div>timeIncrement = double(omeMeta.getPixelsTimeIncrement(0));</div>
<div><br>
</div>
<div>Hope this helps,</div>
<div>Sebastien</div>
<div><br>
<div>
<div>On 6 Jun 2013, at 22:51, Kraft, Lewis James wrote:</div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif">Dear Sebastien,</span></div>
<div style="margin-top:0in; margin-right:0in; margin-left:0in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif"> </span></div>
<div style="margin-top:0in; margin-right:0in; margin-left:0in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif">Today I tried to read an Olympus .oib file. I received the following error which I traced back to the following line of code:</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">time(index1)=double(omeMeta.getPlaneDeltaT(0,index1-1));</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:red">Java exception occurred:</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:red">java.lang.IndexOutOfBoundsException: Index: 0, Size: 0</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:red"> </span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:red"> at java.util.ArrayList.RangeCheck(Unknown Source)</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:red"> </span></div>
<div style="margin-top:0in; margin-right:0in; margin-left:0in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif; text-indent:0.5in">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:red"> at java.util.ArrayList.get(Unknown Source)</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:red"> </span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:red"> at ome.xml.model.Pixels.getPlane(Pixels.java:600)</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:red"> </span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:red"> at loci.formats.ome.OMEXMLMetadataImpl.getPlaneDeltaT(OMEXMLMetadataImpl.java:3631)</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:red"> </span></div>
<div style="margin-top:0in; margin-right:0in; margin-left:0in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif">Do you have any ideas on what might have gone wrong?</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif"> </span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif">Thanks much,</span></div>
<div style="margin-top:0in; margin-right:0in; margin-left:0in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif">Lewis</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
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<div style="border-right-style:none; border-bottom-style:none; border-left-style:none; border-width:initial; border-color:initial; border-top-style:solid; border-top-color:rgb(181,196,223); border-top-width:1pt; padding-top:3pt; padding-right:0in; padding-bottom:0in; padding-left:0in">
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<b><span style="font-size:10pt; font-family:Tahoma,sans-serif">From:</span></b><span style="font-size:10pt; font-family:Tahoma,sans-serif"><span class="Apple-converted-space"> </span>Kraft, Lewis James<span class="Apple-converted-space"> </span><br>
<b>Sent:</b><span class="Apple-converted-space"> </span>Friday, May 31, 2013 4:42 PM<br>
<b>To:</b><span class="Apple-converted-space"> </span>'Sebastien Besson'<br>
<b>Subject:</b><span class="Apple-converted-space"> </span>RE: [ome-users] Nikon ND2 Time information</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Dear Sebastien,</span></div>
<div style="margin-top:0in; margin-right:0in; margin-left:0in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
<div style="margin-top:0in; margin-right:0in; margin-left:0in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Ah Ha! You are exactly correct! Many thanks!</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
<div style="margin-top:0in; margin-right:0in; margin-left:0in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Cheers,</span></div>
<div style="margin-top:0in; margin-right:0in; margin-left:0in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Lewis</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
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<div style="border-right-style:none; border-bottom-style:none; border-left-style:none; border-width:initial; border-color:initial; border-top-style:solid; border-top-color:rgb(181,196,223); border-top-width:1pt; padding-top:3pt; padding-right:0in; padding-bottom:0in; padding-left:0in">
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<b><span style="font-size:10pt; font-family:Tahoma,sans-serif">From:</span></b><span style="font-size:10pt; font-family:Tahoma,sans-serif"><span class="Apple-converted-space"> </span>Sebastien Besson [<a href="mailto:s.besson@dundee.ac.uk" style="color:blue; text-decoration:underline">mailto:s.besson@dundee.ac.uk</a>]<span class="Apple-converted-space"> </span><br>
<b>Sent:</b><span class="Apple-converted-space"> </span>Friday, May 31, 2013 4:41 PM<br>
<b>To:</b><span class="Apple-converted-space"> </span>Kraft, Lewis James<br>
<b>Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] Nikon ND2 Time information</span></div>
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Hi Lewis,</div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
This is because the series and the plane index are 0-based. So to retrieve the first plane of the first series, try</div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">deltaT = double(omeMeta.getPlaneDeltaT(0,0))</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Cheers,</span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Sebastien</span></div>
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On 31 May 2013, at 22:33, Kraft, Lewis James wrote:</div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif">Thanks for the replies! Forgive me, for I am a bit clueless about the Java part of the programming, I tried the following:</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">>> deltaT = double(omeMeta.getPlaneDeltaT(1,1))</span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Java exception occurred:</span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">java.lang.IndexOutOfBoundsException: Index: 1, Size: 1</span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> at java.util.ArrayList.RangeCheck(Unknown Source)</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> at java.util.ArrayList.get(Unknown Source)</span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> at ome.xml.model.OME.getImage(OME.java:600)</span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> at loci.formats.ome.OMEXMLMetadataImpl.getPlaneDeltaT(OMEXMLMetadataImpl.java:3631)</span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif">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?</span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif"> </span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span style="font-size:11pt; font-family:Calibri,sans-serif">Best,</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif">Lewis Kraft</span></div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
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<div style="border-right-style:none; border-bottom-style:none; border-left-style:none; border-width:initial; border-color:initial; border-top-style:solid; padding-top:3pt; padding-right:0in; padding-bottom:0in; padding-left:0in; border-width:initial; border-color:initial">
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<b><span style="font-size:10pt; font-family:Tahoma,sans-serif">From:</span></b><span class="apple-converted-space"><span style="font-size:10pt; font-family:Tahoma,sans-serif"> </span></span><span style="font-size:10pt; font-family:Tahoma,sans-serif">Sebastien
Besson [<a href="mailto:s.besson@dundee.ac.uk" style="color:blue; text-decoration:underline">mailto:s.besson@dundee.ac.uk</a>]<span class="apple-converted-space"> </span><br>
<b>Sent:</b><span class="apple-converted-space"> </span>Friday, May 31, 2013 2:56 PM<br>
<b>To:</b><span class="apple-converted-space"> </span>Curtis Rueden<br>
<b>Cc:</b><span class="apple-converted-space"> </span>Kraft, Lewis James;<span class="apple-converted-space"> </span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color:blue; text-decoration:underline">ome-users@lists.openmicroscopy.org.uk</a><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] Nikon ND2 Time information</span></div>
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<div style="margin-top:0in; margin-right:0in; margin-left:0.5in; margin-bottom:0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
Hi Lewis,</div>
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with your variable names, you should be able to use the following to extract the timestamp of the plane iPlane for the series iSeries:</div>
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deltaT = double(omeMeta.getPlaneDeltaT(iSeries, iPlane));</div>
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As Curtis said, if this call leads to an error, you can send a sample file.</div>
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Regards,</div>
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Sebastien</div>
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On 31 May 2013, at 20:42, Curtis Rueden wrote:</div>
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Hi Lewis,</div>
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> Where can I find this time information for each image plane in the</div>
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> .nd2 files?</div>
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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.</div>
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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" style="color:blue; text-decoration:underline">http://qa.openmicroscopy.org.uk/qa/upload/</a>),
we can work on fixing the problem.</div>
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Regards,</div>
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Curtis</div>
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On Fri, May 31, 2013 at 2:35 PM, Kraft, Lewis James <<a href="mailto:lewis.j.kraft@vanderbilt.edu" target="_blank" style="color:blue; text-decoration:underline">lewis.j.kraft@vanderbilt.edu</a>> wrote:</p>
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Hello,</div>
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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:</div>
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<span style="color:rgb(79,129,189)">imgdata=bfopen(‘fullfilepath\*.nd2’); %command for opening images using BioFormats MATLAB scripts</span></div>
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<span style="color:rgb(79,129,189)">img=imgdata{1,1}{1,1}; %First image in the timeseries</span></div>
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<span style="color:rgb(79,129,189)">metadata=imgdata{1,2}; %Metadata in the .nd2 file</span></div>
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<span style="color:rgb(79,129,189)">omeMeta = imgdata{1, 4}; %OME Metadata</span></div>
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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?</div>
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Thanks much,</div>
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Lewis Kraft</div>
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<span style="font-size:13.5pt; font-family:Helvetica,sans-serif; color:black">Dr Sébastien Besson</span></div>
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<span style="font-size:13.5pt; font-family:Helvetica,sans-serif; color:black">Open Microscopy Environment / Harvard Medical School</span></div>
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<span style="font-size:13.5pt; font-family:Helvetica,sans-serif; color:black">Wellcome Trust Centre for Gene Regulation and Expression,</span></div>
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<span style="font-size:13.5pt; font-family:Helvetica,sans-serif; color:black">College of Life Sciences, University of Dundee, Dow Street,</span></div>
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<span style="font-size:13.5pt; font-family:Helvetica,sans-serif; color:black">Dundee DD1 5EH Scotland UK Tel: (01382) 386364</span></div>
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<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span></div>
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<span style="font-size:13.5pt; font-family:Helvetica,sans-serif; color:black">Dr Sébastien Besson</span></div>
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<span style="font-size:13.5pt; font-family:Helvetica,sans-serif; color:black">Open Microscopy Environment / Harvard Medical School</span></div>
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<span style="font-size:13.5pt; font-family:Helvetica,sans-serif; color:black">Wellcome Trust Centre for Gene Regulation and Expression,</span></div>
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<span style="font-size:13.5pt; font-family:Helvetica,sans-serif; color:black">College of Life Sciences, University of Dundee, Dow Street,</span></div>
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<span style="font-size:13.5pt; font-family:Helvetica,sans-serif; color:black">Dundee DD1 5EH Scotland UK Tel: (01382) 386364</span></div>
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<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span></div>
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<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
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<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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