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Dear Michael,
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<div class="">thanks for the additional troubleshooting. I also retested your sample file with the fix mentioned</div>
<div class="">by David in his previous email but the incorrect dimension detection persists. It looks like more</div>
<div class="">investigation and work will be required to address this problem.</div>
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<div class="">I have record the bug alongside similar issues of the same kind in our Bio-Formats backlog [1]</div>
<div class="">where future progress on the resolution of this issue can be tracked.</div>
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<div class="">Best regards,</div>
<div class="">Sebastien</div>
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<div class="">[1] <a href="https://trello.com/c/LEjj3O3A/281-nd2-timepoints-are-split-into-series" class="">https://trello.com/c/LEjj3O3A/281-nd2-timepoints-are-split-into-series</a></div>
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<div class="">On 14 Sep 2018, at 21:29, Cammer, Michael <<a href="mailto:Michael.Cammer@NYULANGONE.ORG" class="">Michael.Cammer@NYULANGONE.ORG</a>> wrote:</div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">We tried all four combinations of checkboxes of Nikon & Chunkmap and same results.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Cheers-<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Michael<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<b class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>><span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>David Gault (Staff)<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Thursday, September 13, 2018 5:53 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] nd2 files opening with multiple series instead of time series<o:p class=""></o:p></span></div>
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Hi Michael,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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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=" style="color: purple; text-decoration: underline;" class="">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=" style="color: purple; text-decoration: underline;" class="">https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/options.html</a>.<o:p class=""></o:p></div>
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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=" style="color: purple; text-decoration: underline;" class="">https://www.openmicroscopy.org/qa2/qa/upload/</a> would
be great.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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With Thanks,<o:p class=""></o:p></div>
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David Gault<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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On 12 Sep 2018, at 22:52, Cammer, Michael <<a href="mailto:Michael.Cammer@NYULANGONE.ORG" style="color: purple; text-decoration: underline;" class="">Michael.Cammer@NYULANGONE.ORG</a>> wrote:<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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 class=""></o:p></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
</div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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 class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Also, the title is doubled.</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thank you!</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Best regards,</span><o:p class=""></o:p></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Michael Cammer</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">The macro to fix the problem afterwards:</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-family: Calibri, sans-serif;" class=""> t = getTitle;</span><o:p class=""></o:p></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-family: Calibri, sans-serif;" class=""> run("Concatenate...", "all_open title=[nmg smc_xy1] open");</span><o:p class=""></o:p></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-family: Calibri, sans-serif;" class=""> run("Stack to Hyperstack...", "order=xyczt(default) channels=2 slices=31 frames=37 display=Composite");</span><o:p class=""></o:p></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-family: Calibri, sans-serif;" class=""> rename(t);</span><o:p class=""></o:p></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-family: Calibri, sans-serif;" class=""> // manually edit title on save</span><o:p class=""></o:p></div>
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