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Hi Aaron,
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<div class="">Does this issue occur both with and without the chunk map option enabled?</div>
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<div class="">In FIJI you can change the option for ND2 files to use the chunk map table by setting the it as below: </div>
<div class="">Plugins > Bio-Formats > Bio-Formats Plugins Configuration > Formats > Nikon ND2 > Chunkmap</div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<div class="">On 8 Aug 2018, at 12:46, Ponti Aaron <<a href="mailto:aaron.ponti@bsse.ethz.ch" class="">aaron.ponti@bsse.ethz.ch</a>> wrote:</div>
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Hi, everyone<o:p class=""></o:p></div>
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We recently observed that multi-position, multi-color, time-lapse ND2 files generated by the NIS Elements software (version V5.02.00 build 1266 Patch 03 LO, 64bit) on a Nikon Ti2 microscope are not parsed correctly by bioformats (version 5.9.0 included).<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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To better explain the issue, let’s consider an example dataset we recently acquired: it is a 120-position (series), 16-timepoint, 2-channel, 1-plane dataset. (I would like to upload it, if you can give me the coordinates of your FTP server.)<o:p class=""></o:p></div>
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Bioformats correctly lists 120 series, each with T = 16, C = 2, Z = 1 but when opening series = 1 and going through T = 1 to 16, bioformats incorrectly loads the images corresponding to T = 1 for series 1 through 16 instead (in other words, series and time
indices are swapped). This can easily be seen by browsing the dataset in Fiji vs. NIS Elements.<o:p class=""></o:p></div>
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Thanks in advance for looking into it. Please let me know how to provide you with the example dataset (~ 8GB).<o:p class=""></o:p></div>
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a2<o:p class=""></o:p></div>
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<span style="color: rgb(31, 73, 125);" class="">Dr. Aaron Ponti<o:p class=""></o:p></span></div>
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<span style="color: rgb(31, 73, 125);" class="">Software and Data Management Engineer<o:p class=""></o:p></span></div>
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<span style="color: rgb(31, 73, 125);" class="">Image Analysis Specialist<o:p class=""></o:p></span></div>
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<span style="color: rgb(31, 73, 125);" class="">Department of Biosystems Science and Engineering (D-BSSE)<o:p class=""></o:p></span></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">ETH Zürich<o:p class=""></o:p></span></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class=""><a href="mailto:aaron.ponti@bsse.ethz.ch" style="color: rgb(149, 79, 114); text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">aaron.ponti@bsse.ethz.ch</span></a><o:p class=""></o:p></span></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">T: +41 61 387 33 74<o:p class=""></o:p></span></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">F: +41 61 387 39 93<o:p class=""></o:p></span></div>
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