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Hi David

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<div class="">by chance I found on a colleagues computer with an old version of Fiji and Bio-Formats, that the reading of the nd2 files did not cause any problems. </div>

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<div class="">working version (of my colleague)</div>

<div class="">ImageJ 1.51.n (Java 1.8.0_66)</div>

<div class="">Bio-Formats 5.7.0</div>

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<div class="">the version I used submitting this report:</div>

<div class="">ImageJ 1.52g (Java 1.8.0_44)</div>

<div class="">Bio-Formats: 5.9.2</div>

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<div>So there seems to be a regression from 5.7.0 to 5.9.2</div>

<div>However I did not investigate the versions in between…</div>

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<div>Best regards, </div>

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<div>Felix</div>

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<div class="">On 27 Sep 2018, at 16:01 , David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk" class="">d.gault@dundee.ac.uk</a>> wrote:</div>

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Hi Felix,

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<div class="">Thank you for reporting this problem and providing a sample file. I have been able to test and reproduce the issue as you described and it does indeed appear to be a bug.</div>

<div class="">I have opened a Trello card on the Bio-Formats board with the details and some of the initial investigation:</div>

<div class=""><a href="https://trello.com/c/EtOwZ7MH/283-nd2-incorrect-channels-and-pixel-data" class="">https://trello.com/c/EtOwZ7MH/283-nd2-incorrect-channels-and-pixel-data</a></div>

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<div class="">With Thanks,</div>

<div class="">David Gault</div>

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<div class="">On 26 Sep 2018, at 09:28, MEYENHOFER Felix <<a href="mailto:felix.meyenhofer@unifr.ch" class="">felix.meyenhofer@unifr.ch</a>> wrote:</div>

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<div class="">Dear OMERO Team</div>

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<div class="">The following image causes problems when I try to open it using Fiji and Bio-Formats. Bellow is the image shown with the NIS Elements Viewer.</div>

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<div class=""><span id="cid:4C227BF7-AFCF-4F34-BC43-8CFA06A07595@unifr.ch" class=""><Screen Shot 2018-09-26 at 10.14.16.png></span></div>

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<div class="">The window that is produced by Fiji shows only a part of the original image.</div>

<div class=""><span id="cid:8223363A-CA51-4152-BA6F-C7960B94687B@unifr.ch" class=""><Screen Shot 2018-09-26 at 10.17.13.png></span></div>

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<div class="">A closer look, shows that the C and X-Y dimensions seem to be messed up. </div>

<div class=""><span id="cid:3B937C8B-A2AF-4D4E-82AE-13315677484B@unifr.ch" class=""><Screen Shot 2018-09-26 at 10.17.34.png></span></div>

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Finally the parsing of the metadata seems to have trouble too, given that the colors are not coherent with the image acquisition and given that the scale factor too seems to be missing in the displayed image in Fiji.<br class="">

The original file can be found in the following link:<br class="">

<a href="https://drive.switch.ch/index.php/s/QsroyTOOq6cDQXy" class="">https://drive.switch.ch/index.php/s/QsroyTOOq6cDQXy</a><br class="">

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<div class="">Is there a work-around, or could you confirm this being a bug?</div>

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<div class="">Best regards, </div>

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Felix </div>

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<span style="font-size:10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>

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