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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">We gave up on BioFormats for opening ND2 files more than a few hundred MB. We now have files that are 10+ GB and they don’t open, or maybe they do but we don’t
have the patience to wait. It’s faster to export folders of TIFs from Elements and reassemble.
<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">We’d love to see ND2 importer working for large files.<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>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#7030A0">Michael Cammer,
</span></b><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Sr Research Scientist</span><b><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#7030A0">,
</span></b><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">DART Microscopy Laboratory</span><b><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#7030A0"><o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:black">NYU Langone Health, 540</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> First Avenue, SK2 Microscopy Suite, New York, NY
10016<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">C: 914-309-3270
</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#7030A0"><a href="mailto:Michael.Cammer@med.nyu.edu"><span style="color:#7030A0">Michael.Cammer@med.nyu.edu</span></a>
<a href="http://nyulmc.org/micros">http://nyulmc.org/micros</a> <a href="http://microscopynotes.com/">
<span style="color:#7030A0">http://microscopynotes.com/</span></a> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#7030A0"><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>Paul-Gilloteaux Perrine<br>
<b>Sent:</b> Thursday, February 8, 2018 9:31 AM<br>
<b>To:</b> ome-users@lists.openmicroscopy.org.uk<br>
<b>Cc:</b> francois.paris@univ-nantes.fr; perrine.paul-gilloteaux@univ-nantes.fr; Isabelle.Delias@nikon.com; manon.pietri@univ-nantes.fr<br>
<b>Subject:</b> [ome-users] Bio-Formats ND2 importer bug<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p><span style="font-family:"Calibri","sans-serif";color:black">Dear Bio-Formats team,<o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">Im also reporting a bug on nd2 with bioformat (tested on last release 5.7.3 snapshot and previous)<o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">Disabling the chunkmap option does not solve the problem.<o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">I ve uploaded a short example data set here:
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.openmicroscopy.org_qa2_qa_feedback_20512_-3Ftoken-3D1f4ad9c32a8ea3de4f0c34d2c4add35c&d=DwMFAw&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=wOsSGQja4TLs56sXa1P8sT_q6DdHNaWJvRr50dHM4U4&s=LH49R6mHp1j5M6bwJ4YyuzFZ7TNHPps6IrWr_9OqwIs&e=" id="LPlnk724034">
https://www.openmicroscopy.org/qa2/qa/feedback/20512/?token=1f4ad9c32a8ea3de4f0c34d2c4add35c</a><o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">In a few words (see my comments on the link above), time and positions are shuffled, while NIS element correcty read the file metadata.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">Series corresponds to time when it should be position, and time to what should be position.<br>
It only happens when there is several channels (no problem if the movie is 1 channel multi-t, multi pos)<br>
It only happens with acquisitions generated with the last version of NIS 4.5.0.00 (but read correctly by previous version of NIS element).<br>
Best regards,<br>
Perrine<o:p></o:p></span></p>
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