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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">We tried all four combinations of checkboxes of Nikon & Chunkmap and same results.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Cheers-<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Michael<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:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ome-users <ome-users-bounces@lists.openmicroscopy.org.uk>
<b>On Behalf Of </b>David Gault (Staff)<br>
<b>Sent:</b> Thursday, September 13, 2018 5:53 AM<br>
<b>To:</b> OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>
<b>Subject:</b> Re: [ome-users] nd2 files opening with multiple series instead of time series<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">Thank you for sending in the report. This sounds like it may be related to a similar problem which we have recently put in place a fix for (<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_openmicroscopy_bioformats_pull_3191&d=DwMGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=f6LzGbXPPsRXRCRm9Of4so8BlLZqNxm-xuaHes0NUCU&s=cFL3TWfZD8iIg5bKQlBtw_-i96aMQJwS72SvonJ374Y&e=">https://github.com/openmicroscopy/bioformats/pull/3191</a>).
A short term workaround until this is released would be to disable the use of the native chunk map for ND2 files, you can see how to set the options in <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.openmicroscopy.org_bio-2Dformats_5.9.2_formats_options.html&d=DwMGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=f6LzGbXPPsRXRCRm9Of4so8BlLZqNxm-xuaHes0NUCU&s=3o3lW8c2BlwCxe4nv96Q0GZMYbVFy5BtvsR9FeoyvWs&e=">https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/options.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">If you are still seeing the issue with the chunk map disabled then this is a separate issue, in which case uploading a sample file to <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.openmicroscopy.org_qa2_qa_upload_&d=DwMGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=f6LzGbXPPsRXRCRm9Of4so8BlLZqNxm-xuaHes0NUCU&s=iQ_EfJa4bZFwsS_g7hkKvEbyxbvtHJo-vHXOvsDHpcI&e=">https://www.openmicroscopy.org/qa2/qa/upload/</a> would
be great.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">With Thanks,<o:p></o:p></p>
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<p class="MsoNormal">David Gault<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 12 Sep 2018, at 22:52, Cammer, Michael <<a href="mailto:Michael.Cammer@NYULANGONE.ORG">Michael.Cammer@NYULANGONE.ORG</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"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Last week we used a Nikon W1 spinning disk system. 2 channel Z series were taken at multiple positions through time. Each XY location is a separate ND2 file.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">When we open them with BioFormats 5.9.2 with jave 1.8, we are prompted for Series whereas they should be a single file of timepoints. It’s easy to combine them
with the macro below, but would be great to have them open as a single time series. Happy to upload an example file if you would like.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Also, the title is doubled.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thank you!</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best regards,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Michael Cammer</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The macro to fix the problem afterwards:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif"> t = getTitle;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif"> run("Concatenate...", "all_open title=[nmg smc_xy1] open");</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif"> run("Stack to Hyperstack...", "order=xyczt(default) channels=2 slices=31 frames=37 display=Composite");</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif"> rename(t);</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif"> // manually edit title on save</span><o:p></o:p></p>
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<p class="MsoNormal"><br>
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