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Hi Maximilian,
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<div class="">One test that would be worth carrying out would be to try the import with the new chunk map configuration switched off to see if the import gives a different result.</div>
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<div class="">With the latest release of Bio-Formats there is a configurable option to use the chunk map table to improve performance. This can be configured via a checkbox in the following dialog:</div>
<div class=""><b class="">Plugins -> Bio-Fromats -> Bio-Formats Plugins Configuration -> Nikon ND2</b></div>
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<div class="">Would you be able to confirm if this still results in the same issue?</div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<div class="">On 28 Mar 2017, at 11:06, Maximilian Fries <<a href="mailto:MF474@MRC-CU.cam.ac.uk" class="">MF474@MRC-CU.cam.ac.uk</a>> wrote:</div>
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Dear list,<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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I have a 60GB .nd2 file generated using NIS runnin a Nikon microscope. It is a multi-point (25 xy positions), multi-channel (4 channels) time lapse (54 time points). When I open it with BioFormats 5.4 as part of Fjii/ImageJ (2.0.0-rc-59/1.51k; Java 1.8.0_66
on Windows 8.1, 64-bit), it shows all 25 xy positions in the importer window, but the stack that opens for a point is actually not from one position, but each time point is from a different position. I presume that xy is treated as t and vice versa.<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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I have attached a screenshot of the nd2 opened in NIS Elements to illustrate the structure.<o:p class=""></o:p></div>
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I am not sure whether this is an actual bug or user error. If it is the latter, my apologies, but I would still very much appreciate any support.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Many thanks,<o:p class=""></o:p></div>
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Max<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span class=""><image002.jpg></span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span style="" class="">--<br class="">
Maximilian Fries<o:p class=""></o:p></span></div>
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<span style="" class="">PhD student<o:p class=""></o:p></span></div>
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<span style="" class=""> </span></div>
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<span style="" class="">Venkitaraman Group<br class="">
</span><span class="">MRC Cancer Unit - University of Cambridge<o:p class=""></o:p></span></div>
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<span class="">Hutchison/MRC Research Centre<o:p class=""></o:p></span></div>
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<span class="">Box 197, Biomedical Campus<br class="">
Cambridge<o:p class=""></o:p></span></div>
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<span class="">United Kingdom<o:p class=""></o:p></span></div>
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<span class="">CB2 0XZ<o:p class=""></o:p></span></div>
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<span style="font-size: 10pt;" class=""> </span></div>
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<span style="" class="">E-Mail:<span class="Apple-converted-space"> </span><a href="mailto:mf474@mrc-cu.cam.ac.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class=""><span style="color: blue;" class="">mf474@mrc-cu.cam.ac.uk</span></a><o:p class=""></o:p></span></div>
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<span style="" class="">+44 (0) 1223 763376 (office)<o:p class=""></o:p></span></div>
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<span class=""><span id="cid:image006.jpg@01D2A7B3.643E1320"><image006.jpg></span><o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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