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<div>Hi Lewis,</div>
<div><br>
</div>
<div>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>
<div>
<div><br>
</div>
<div>deltaT = double(omeMeta.getPlaneDeltaT(iSeries, iPlane));</div>
<div><br>
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<div>As Curtis said, if this call leads to an error, you can send a sample file.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Sebastien</div>
<div><br>
</div>
<div>
<div>
<div>On 31 May 2013, at 20:42, Curtis Rueden wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr">Hi Lewis,
<div><br>
</div>
<div>
<div>> Where can I find this time information for each image plane in the</div>
<div>> .nd2 files?</div>
<div><br>
</div>
<div>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>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Curtis</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Fri, May 31, 2013 at 2:35 PM, Kraft, Lewis James <span dir="ltr">
<<a href="mailto:lewis.j.kraft@vanderbilt.edu" target="_blank">lewis.j.kraft@vanderbilt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin-top:0px; margin-right:0px; margin-bottom:0px; margin-left:0.8ex; border-left-width:1px; border-left-color:rgb(204,204,204); border-left-style:solid; padding-left:1ex; position:static; z-index:auto">
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<p class="MsoNormal">Hello,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="color:#4f81bd">imgdata=bfopen(‘fullfilepath\*.nd2’); %command for opening images using BioFormats MATLAB scripts<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#4f81bd"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:#4f81bd">img=imgdata{1,1}{1,1}; %First image in the timeseries<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#4f81bd"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:#4f81bd">metadata=imgdata{1,2}; %Metadata in the .nd2 file<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#4f81bd"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:#4f81bd">omeMeta = imgdata{1, 4}; %OME Metadata<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thanks much,<u></u><u></u></p>
<p class="MsoNormal">Lewis Kraft<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
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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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