<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hey David
<div class=""><br class="">
</div>
<div class="">so here is the file that made me believe:</div>
<div class=""><a href="https://drive.switch.ch/index.php/s/zgxUk4c98loQTQJ" class="">https://drive.switch.ch/index.php/s/zgxUk4c98loQTQJ</a> </div>
<div class=""><br class="">
</div>
<div class="">it turns out the file above is 3x8bit and the file I sent initially is 9x8bit. So a normal RGB works (BF swaps green and red though). </div>
<div class="">Bio-Formats does seem to have trouble when each channel is saved in RGB. </div>
<div class=""><br class="">
</div>
<div class="">Given that both images come from the save instrument I jumped to the conclusion that the BF version of my colleague might have an impact, which was indeed different. I should have checked how the images are different given that one is 3 times
lighter - dah - my bad, should have done that test before making claims, sorry. </div>
<div class=""><br class="">
</div>
<div class="">Best</div>
<div class=""><br class="">
</div>
<div class="">Felix</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 12 Oct 2018, at 14:48 , David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk" class="">d.gault@dundee.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Felix,
<div class=""><br class="">
</div>
<div class="">Thank you for the update, we have made a number of updates to the nd2 reader in that time, especially in the 5.7 releases, so it may be possible that there is a regression. </div>
<div class="">I retested the original file that you had linked with 5.7.0 and a number of other releases but the issue still appears to be present in that particular file, would you be able to test if that file works as expected on your colleagues setup?</div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 12 Oct 2018, at 08:55, MEYENHOFER Felix <<a href="mailto:felix.meyenhofer@unifr.ch" class="">felix.meyenhofer@unifr.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi David
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<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>
<div class="">
<div class=""><br class="">
</div>
<div class="">So there seems to be a regression from 5.7.0 to 5.9.2</div>
<div class="">However I did not investigate the versions in between…</div>
<div class=""><br class="">
</div>
<div class="">Best regards, </div>
<div class=""><br class="">
</div>
<div class="">Felix</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<blockquote type="cite" class="">
<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>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Felix,
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<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>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
<div class="">Dear OMERO Team</div>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
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="">
<div class=""><br class="webkit-block-placeholder">
</div>
<div class="">Is there a work-around, or could you confirm this being a bug?</div>
<div class=""><br class="">
</div>
<div class="">Best regards, </div>
<div class=""><br class="">
Felix </div>
</div>
_______________________________________________<br class="">
ome-users mailing list<br class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br class="">
<span style="font-size:10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
_______________________________________________<br class="">
ome-users mailing list<br class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
_______________________________________________<br class="">
ome-users mailing list<br class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br class="">
<span style="font-size:10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
_______________________________________________<br class="">
ome-users mailing list<br class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</body>
</html>