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<p class="MsoNormal"><span style="color:#1F497D">I can check the version on the computer.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I upgraded both IJ and LOCI to daily builds last Thurs or Friday.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">No error messages. Simply stops as though the whole thing worked fine.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I was opening as a standard hyperstack. IJ has 48GB allocated to it on a computer with 192GB. When we export to TIF from the Nikon software, we can open the entire 17GB dataset and do everything we want.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I can put the dataset on your ftp server.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">We also have similar problems with big CZI files. For instance, tiling 3 X2 opens fine, but 100+ tiles pops up a message asking us for a range of tiles we want opened and then displays nothing useful.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">=========================================================================<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D"> Cell: 914-309-3270 **
</span><b><span style="font-size:10.0pt;font-family:"Adobe Fan Heiti Std B","sans-serif";color:#1F497D">MY OFFICE HAS MOVED TO SKIRBALL 2<sup>nd</sup> FLOOR, Back right **</span></b><i><span style="font-size:10.0pt;color:#1F497D"><o:p></o:p></span></i></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D"> <a href="http://ocs.med.nyu.edu/microscopy">
http://ocs.med.nyu.edu/microscopy</a> & <a href="http://microscopynotes.com/">http://microscopynotes.com/</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><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""> ome-users [mailto:ome-users-bounces@lists.openmicroscopy.org.uk]
<b>On Behalf Of </b>Sebastien Besson (Staff)<br>
<b>Sent:</b> Tuesday, September 22, 2015 4:01 PM<br>
<b>To:</b> users OME<br>
<b>Subject:</b> Re: [ome-users] .nd2 files bug<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Michael, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">thanks for your feedback.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Reading through your email, I suppose you are opening your nd2 files<o:p></o:p></p>
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<p class="MsoNormal">using ImageJ. Which version of Bio-Formats did you download and use<o:p></o:p></p>
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<p class="MsoNormal">for opening the files?<o:p></o:p></p>
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<p class="MsoNormal">Also when the file opening stops, do you receive a warning or an<o:p></o:p></p>
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<p class="MsoNormal">error message or does the application exit?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Assuming the dataset started to load correctly, there might be a memory<o:p></o:p></p>
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<p class="MsoNormal">issue. This page of the Bio-Formats user documentation [1] provides<o:p></o:p></p>
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<p class="MsoNormal">some suggestions for dealing with large datasets. Is the dataset loaded<o:p></o:p></p>
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<p class="MsoNormal">using the virtual stack for instance?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best regards,<o:p></o:p></p>
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<p class="MsoNormal">Sebastien<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">[1] <a href="https://www.openmicroscopy.org/site/support/bio-formats5.1/users/imagej/managing-memory.html">https://www.openmicroscopy.org/site/support/bio-formats5.1/users/imagej/managing-memory.html</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 22 Sep 2015, at 17:39, Cammer, Michael <<a href="mailto:Michael.Cammer@med.nyu.edu">Michael.Cammer@med.nyu.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">We are having a problem opening .nd2 files.<o:p></o:p></p>
<p class="MsoNormal">We have this problem is an older version of LOCI and a daily build we downloaded late last week.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Each file is 17.8 GB with 55 timepoints of 2 channels of 15 Z positions.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">LOCI opens the first 27 timepoints, 2 channels, and 7 Z of the 28<sup>th</sup> timepoint and then just stops.
<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">If we export the file from Nikon Elements to OME TIFF, the whole thing can be operated on fine, but it would be preferable to be able to open directly into ImageJ.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Thank you.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt">=========================================================================</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt">Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt"> Cell: 914-309-3270 **
</span><b><span style="font-size:10.0pt;font-family:"Adobe Fan Heiti Std B","sans-serif"">MY OFFICE HAS MOVED TO SKIRBALL 2<sup>nd</sup> FLOOR, Back right **</span></b><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt"> <a href="http://ocs.med.nyu.edu/microscopy">
http://ocs.med.nyu.edu/microscopy</a> & <a href="http://microscopynotes.com/">http://microscopynotes.com/</a></span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
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