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<div class="">Hi Kaustav,</div>
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<div class="">Thank you for reporting this issue, I have created a Trello card on the Bio-Formats inbox to track the issue <a href="https://trello.com/c/IpwZ4EGO/224-nd2-merged-z-and-t" class="">https://trello.com/c/IpwZ4EGO/224-nd2-merged-z-and-t</a>. </div>
<div class="">To help us troubleshoot the problem it would be great if you could upload the file to <a href="https://www.openmicroscopy.org/qa2/qa/upload/" class="">https://www.openmicroscopy.org/qa2/qa/upload/</a></div>
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With Thanks,
<div class="">David Gault</div>
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<blockquote type="cite" class="">
<div class="">On 23 Feb 2018, at 10:00, Straatman, Kees (Dr.) <<a href="mailto:krs5@LEICESTER.AC.UK" class="">krs5@LEICESTER.AC.UK</a>> wrote:</div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Dear Kaustav,<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="">One option that might work is go to Image > Hyperstack > Stack to Hyperstack and see if you can find a setting that will organize the images in the correct order.
Another option might be to export the files to a different format in the ND viewer like ICS/IDS and see if these open correctly in Fiji.<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: 0cm 0cm 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="">Also, occasionally images open differently when opened directly in the Bio-Formats plugin (Plugins > Bio-Formats > Bio-Formats Importer) compared to File > Open.<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="">Best wishes<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="">Kees<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: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Dr Ir K.R. Straatman<br class="">
Senior Experimental Officer<o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Advanced Imaging Facility<o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Centre for Core Biotechnology Services<br class="">
University of Leicester<br class="">
<a href="http://www.le.ac.uk/advanced-imaging-facility" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">www.le.ac.uk/advanced-imaging-facility</a><o:p class=""></o:p></span></div>
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</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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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
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<b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span lang="EN-US" 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: rgb(149, 79, 114); text-decoration: underline;" class="">mailto: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>Kaustav Bera<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>22 February 2018 20:09<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:kaustav0bera@gmail.com" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">kaustav0bera@gmail.com</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>[ome-users] Problem opening <dot>nd2 file using FIJI<o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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<span style="font-family: Calibri, sans-serif;" class="">Hi!<o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class=""> </span></div>
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<span style="font-family: Calibri, sans-serif;" class="">I am trying to open a file acquired by Nikon A1 confocal system using FIJI. I have updated both the FIJI and the bioformats plugin before opening the file. Its a z stack at 8 different time points and
two different channels. When I open it using FIJI the file opens with the two channels as expected but the z stacks and the time points are all merged as a time sequence. However when I open the file using NIS Viewer, both the metadata and the image are displayed
properly. Please find attached some screen-shots for your kind referral.<o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class="">Any suggestions to curtail this problem will be highly appreciated. I can also forward the particular file if required.<o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class=""> </span></div>
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<em class=""><b class=""><span style="font-family: Calibri, sans-serif;" class="">System info:</span></b></em><span style="font-family: Calibri, sans-serif;" class=""><o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class="">Operating System: Windows 7 Professional edition​<o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class=""> </span></div>
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<span style="font-family: Calibri, sans-serif;" class="">Thanks and regards,<o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class="">Kaustav Bera<o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class="">Johns Hopkins University<o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class="">Baltimore, MD<o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class="">USA<o:p class=""></o:p></span></div>
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<span style="font-family: Calibri, sans-serif;" class=""> </span></div>
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<span style="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; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">_______________________________________________</span><br style="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; background-color: rgb(255, 255, 255);" class="">
<span style="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; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">ome-users
mailing list</span><br style="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; background-color: rgb(255, 255, 255);" class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: rgb(149, 79, 114); text-decoration: underline; 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; background-color: rgb(255, 255, 255);" class="">ome-users@lists.openmicroscopy.org.uk</a><br style="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; background-color: rgb(255, 255, 255);" class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="color: rgb(149, 79, 114); text-decoration: underline; 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; background-color: rgb(255, 255, 255);" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br style="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; background-color: rgb(255, 255, 255);" class="">
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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