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Hi Michael,
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<div class="">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://github.com/openmicroscopy/bioformats/pull/3191" 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://docs.openmicroscopy.org/bio-formats/5.9.2/formats/options.html" class="">https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/options.html</a>.</div>
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<div class="">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://www.openmicroscopy.org/qa2/qa/upload/" class="">https://www.openmicroscopy.org/qa2/qa/upload/</a> would
be great.</div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<blockquote type="cite" class="">
<div class="">On 12 Sep 2018, at 22:52, Cammer, Michael <<a href="mailto:Michael.Cammer@NYULANGONE.ORG" class="">Michael.Cammer@NYULANGONE.ORG</a>> wrote:</div>
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<div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
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<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.<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=""> </span></div>
<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.<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=""> </span></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.<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=""> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thank you!<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=""> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Best regards,<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 Cammer<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=""> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">The macro to fix the problem afterwards:<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=""> </span></div>
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<span style="font-family: Calibri, sans-serif;" class=""> t = getTitle;<o:p class=""></o:p></span></div>
<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");<o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class=""> run("Stack to Hyperstack...", "order=xyczt(default) channels=2 slices=31 frames=37 display=Composite");<o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class=""> rename(t);<o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class=""> // manually edit title on save</span><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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