<div dir="ltr">Hi Michael,<div><br></div><div>Recent versions of Bio-Formats require Java 7 or later, but your ImageJ is still using Java 6.</div><div><br></div><div>For details on upgrading, see: <a href="https://imagej.net/Java_8">https://imagej.net/Java_8</a></div><div><br></div><div>Regards,</div><div>Curtis</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><span style="font-size:12.8px">--</span></div><div><span style="font-size:12.8px">Curtis Rueden</span><br></div><div><span style="font-size:12.8px">LOCI software architect - <a href="https://loci.wisc.edu/software" target="_blank">https://loci.wisc.edu/software</a></span></div><div>ImageJ2 lead, Fiji maintainer - <span style="font-size:12.8px"><a href="https://imagej.net/User:Rueden" target="_blank">https://imagej.net/User:Rueden</a></span></div><div>Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" target="_blank">http://forum.imagej.net/</a></div><div><br></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Thu, Aug 17, 2017 at 10:45 AM, Cammer, Michael <span dir="ltr"><<a href="mailto:Michael.Cammer@med.nyu.edu" target="_blank">Michael.Cammer@med.nyu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-US" link="blue" vlink="purple">
<div class="m_-8136031225196469418WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Please find below the error I get with the Aug 14 build of bioformats_package<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">ImageJ 1.51p; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 7794K of 12000MB (<1%)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">java.lang.<wbr>UnsupportedClassVersionError: loci/plugins/LociImporter : Unsupported major.minor version 51.0<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at java.lang.ClassLoader.<wbr>defineClass1(Native Method)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at java.lang.ClassLoader.<wbr>defineClassCond(ClassLoader.<wbr>java:632)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at java.lang.ClassLoader.<wbr>defineClass(ClassLoader.java:<wbr>616)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at java.security.<wbr>SecureClassLoader.defineClass(<wbr>SecureClassLoader.java:141)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at java.net.URLClassLoader.<wbr>defineClass(URLClassLoader.<wbr>java:283)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at java.net.URLClassLoader.<wbr>access$000(URLClassLoader.<wbr>java:58)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at java.net.URLClassLoader$1.run(<wbr>URLClassLoader.java:197)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at java.security.<wbr>AccessController.doPrivileged(<wbr>Native Method)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at java.net.URLClassLoader.<wbr>findClass(URLClassLoader.java:<wbr>190)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at java.lang.ClassLoader.<wbr>loadClass(ClassLoader.java:<wbr>307)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at java.lang.ClassLoader.<wbr>loadClass(ClassLoader.java:<wbr>248)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.IJ.runUserPlugIn(IJ.java:<wbr>215)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.IJ.runPlugIn(IJ.java:181)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.IJ.runPlugIn(IJ.java:170)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at HandleExtraFileTypes.<wbr>openImage(<wbr>HandleExtraFileTypes.java:258)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at HandleExtraFileTypes.run(<wbr>HandleExtraFileTypes.java:37)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.IJ.runUserPlugIn(IJ.java:<wbr>217)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.IJ.runPlugIn(IJ.java:181)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.IJ.runPlugIn(IJ.java:170)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.io.Opener.<wbr>openWithHandleExtraFileTypes(<wbr>Opener.java:514)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.io.Opener.openImage(Opener.<wbr>java:368)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.io.Opener.openImage(Opener.<wbr>java:242)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.io.Opener.open(Opener.java:<wbr>109)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.io.Opener.<wbr>openAndAddToRecent(Opener.<wbr>java:291)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.plugin.DragAndDrop.<wbr>openFile(DragAndDrop.java:192)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at ij.plugin.DragAndDrop.run(<wbr>DragAndDrop.java:159)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> at java.lang.Thread.run(Thread.<wbr>java:619)<u></u><u></u></span></p><span class="">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<div>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#7030a0"><u></u> <u></u></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#7030a0">Michael Cammer<u></u><u></u></span></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Research Scientist<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">DART Microscopy Laboratory<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#7030a0">NYU Langone Health<u></u><u></u></span></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">540 First Avenue<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">SK2 Microscopy Suite<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">New York, NY 10016<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">C <a href="tel:(914)%20309-3270" value="+19143093270" target="_blank">914-309-3270</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#7030a0"><a href="mailto:Michael.Cammer@med.nyu.edu" target="_blank"><span style="color:#7030a0">Michael.Cammer@med.nyu.edu</span></a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#7030a0"><a href="https://med.nyu.edu/research/research-resources/scientific-cores-shared-resources/microscopy-laboratory" target="_blank"><span style="color:#7030a0">https://med.nyu.edu/research/<wbr>research-resources/scientific-<wbr>cores-shared-resources/<wbr>microscopy-laboratory</span></a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#7030a0"><a href="http://microscopynotes.com/" target="_blank"><span style="color:#7030a0">http://microscopynotes.com/</span></a>
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
</span><div>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> ome-users [mailto:<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@<wbr>lists.openmicroscopy.org.uk</a>]
<b>On Behalf Of </b>David Gault (Staff)<br>
<b>Sent:</b> Wednesday, August 16, 2017 10:39 AM</span></p><div><div class="h5"><br>
<b>To:</b> OME User Support List<br>
<b>Subject:</b> Re: [ome-users] Two issues with ND2 (Nikon) files<u></u><u></u></div></div><p></p>
</div>
</div><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Hi Michael and Maxime, <u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Thank you for the further clarification and feedback on these issues.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Michael, do you have a screenshot of the exception you were seeing with 5.6.0? Did it occur when opening any CZI image?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">If you had a sample file that was failing which you could upload to the below link that would be very useful for our testing:<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.openmicroscopy.org_qa2_qa_upload_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=N7IILdMFEgZ9CcSE-j5M-XsLdJC2DlI1Yl-r03zAbN8&e=" target="_blank">https://www.openmicroscopy.<wbr>org/qa2/qa/upload/</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">I have updated the Trello card with the additional detail and also with some details on further investigation into one of these issues:<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__trello.com_c_RyXt2BAg_177-2Dnd2-2Dincorrect-2Dchannel-2Dcount&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=W3JexGg4pOU9f1gelmO-i4Hjn2V6jLHSHY26r-VBv9E&e=" target="_blank">https://trello.com/c/RyXt2BAg/<wbr>177-nd2-incorrect-channel-<wbr>count</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">With Thanks,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">David Gault<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On 15 Aug 2017, at 20:17, Cammer, Michael <<a href="mailto:Michael.Cammer@med.nyu.edu" target="_blank">Michael.Cammer@med.nyu.edu</a>> wrote:<u></u><u></u></p>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">We are also having issues with CZI files with 5.6.0.<br>
<br>
The problem appears to be that when we click Stop during a timelapse experiment or if we move the stage while imaging, the images are not saved in the same CZI format as when we don't move the stage and let the experiment complete.<br>
<br>
This image<br>
</span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_temp_bftemp_BioFormatsissue.png&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=11jOOEH8c_ETwyrIBPydYEtEgwl1tquvgLMlzwS-mt0&e=" target="_blank"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">http://microscopynotes.com/<wbr>temp/bftemp/BioFormatsissue.<wbr>png</span></a><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif""><br>
should be a simple color (AxioCam color) time series that fills the window. The sequences that went to completion open fine.<br>
<br>
We have been using 5.1.10-DEV built on 10 May 2016. Today we updated both ImageJ and BioFormats to the daily build and BioFormats always throws an exception. We rolled back to the the May 2010 version.<br>
<br>
Help appreciated.<br>
<br>
Thank you!<br>
<br>
Michael Cammer<br>
Research Scientist<br>
DART Microscopy Laboratory<br>
<br>
NYU Langone Health<br>
540 First Avenue<br>
SK2 Microscopy Suite<br>
New York, NY 10016<br>
<br>
C <a href="tel:(914)%20309-3270" value="+19143093270" target="_blank">914-309-3270</a><br>
</span><a href="mailto:Michael.Cammer@med.nyu.edu" target="_blank"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">Michael.Cammer@med.nyu.edu</span></a><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif""><br>
</span><a href="https://med.nyu.edu/research/research-resources/scientific-cores-shared-resources/microscopy-laboratory" target="_blank"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">https://med.nyu.edu/research/<wbr>research-resources/scientific-<wbr>cores-shared-resources/<wbr>microscopy-laboratory</span></a><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif""><br>
</span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=NQub4TDHShuVa8K3P0LhvNM0OIkaU4HfRRe1G5Zume8&e=" target="_blank"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">http://microscopynotes.com/</span></a><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif""> <br>
<br>
<br>
<br>
-----Original Message-----<br>
From: ome-users [</span><a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">mailto:ome-users-bounces@<wbr>lists.openmicroscopy.org.uk</span></a><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">]
On Behalf Of Maxime Woringer<br>
Sent: Tuesday, August 15, 2017 1:08 PM<br>
To: OME User Support List<br>
Subject: Re: [ome-users] Two issues with ND2 (Nikon) files<br>
<br>
Hi David,<br>
<br>
I confirm that I also encounter the two issues mentioned below using the new BioFormats release (5.6.0).<br>
<br>
Best,<br>
Maxime<br>
<br>
David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk" target="_blank">d.gault@dundee.ac.uk</a>> writes:<br>
<br style="text-align:start;word-spacing:0px">
<br>
</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">Hi Maxime,<br>
<br>
Thank for reporting this issue and for providing sample files to test with.<br>
I can certainly reproduce the first the issue using the sample files provided and this does indeed look to be a bug.<br>
For the second issue I was unable to reproduce using bfconvert from the latest Bio-Formats release, and in theory the conversion should be the same as the FIJI result.<br>
Would you be able to run bfconvert -version to confirm that bftools is using the latest jars?<br>
<br>
I have created a Trello card on the Bio-Formats inbox for further<span class="m_-8136031225196469418apple-converted-space"> </span><br>
investigation into these issues:<span class="m_-8136031225196469418apple-converted-space"> </span><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__trello.com_c_RyXt" target="_blank">https://urldefense.proofpoint.<wbr>com/v2/url?u=https-3A__trello.<wbr>com_c_RyXt</a><br>
2BAg_177-2Dnd2-2Dincorrect-<wbr>2Dchannel-2Dcount&d=DQIBAg&c=<wbr>j5oPpO0eBH1iio<br>
48DtsedbOBGmuw5jHLjgvtN2r4ehE&<wbr>r=oU_05LztNstAydlbm5L5GDu_<wbr>vAdjXk3frDLx_C<br>
qKkuo&m=<wbr>g6CNr9rxiOItnhC2oaw8J5mhdFjCF0<wbr>dh8hsaIy2xIHw&s=_XcwsqhVzEBCf-<wbr>t1<br>
GTD086wg8D-d5f2UMVp16-f5bV8&e=<br>
<br>
With Thanks,<br>
David Gault<br>
<br>
On 14 Aug 2017, at 04:01, Maxime Woringer <<a href="mailto:maxime.woringer@berkeley.edu" target="_blank">maxime.woringer@berkeley.edu</a><<a href="mailto:maxime.woringer@berkeley.edu" target="_blank"><wbr>mailto:maxime.woringer@<wbr>berkeley.edu</a>>> wrote:<br>
<br>
Dear Bio-Formats users/developers,<br>
<br>
I am trying to convert ND2 files (acquired with NIkon NIS elements) to<span class="m_-8136031225196469418apple-converted-space"> </span><br>
TIFF files, ideally in an automated fashion, but I am encountering<span class="m_-8136031225196469418apple-converted-space"> </span><br>
issues that seem to me like bugs (but I'd be happy to be proven wrong).<br>
<br>
1. Some single images appear corrupted when I try to convert them to<span class="m_-8136031225196469418apple-converted-space"> </span><br>
TIFF. Below is an example. The two files (BF007 and BF008) were<span class="m_-8136031225196469418apple-converted-space"> </span><br>
created on the same machine, same software, at a 30' interval. I am<span class="m_-8136031225196469418apple-converted-space"> </span><br>
not aware of any differing setting except the ROI size.<br>
- BF008.nd2 opens properly in Fiji and converts properly using<span class="m_-8136031225196469418apple-converted-space"> </span><br>
bfconvert (laters version). I am attaching the .nd2 file, the<span class="m_-8136031225196469418apple-converted-space"> </span><br>
resulting TIFF file, and the convert log (.txt files) and a screenshot of how Fiji opens it.<br>
- BF008.nd2 opens corrupted in Fiji, and the same result happens using<span class="m_-8136031225196469418apple-converted-space"> </span><br>
bfconvert. It seems that BF thinks it is a 3-channel image (it is not).<br>
<BF007.nd2><BF007.txt><BF007-<wbr>bf.tiff><BF007-Capture du 2017-08-13<span class="m_-8136031225196469418apple-converted-space"> </span><br>
18-50-59.png><BF008.nd2><<wbr>BF008.txt><BF008-bf.tiff><<wbr>BF008-Capture du<span class="m_-8136031225196469418apple-converted-space"> </span><br>
2017-08-13 18-50-53.png> 2. Now moving to ND2 TIFF series (one<span class="m_-8136031225196469418apple-converted-space"> </span><br>
channel, multiple timepoints), they open fine in Fiji using<span class="m_-8136031225196469418apple-converted-space"> </span><br>
BioFormats, however, if I use the following<br>
command:<br>
<br>
bftools/bfconvert in.nd2 out.tiff<br>
<br>
The resulting TIFF file opens totally corrupted in Fiji/ImageJ (note<span class="m_-8136031225196469418apple-converted-space"> </span><br>
that the first frame is fine).<br>
<br>
Below are an example source file (nd2), the conversion result using<span class="m_-8136031225196469418apple-converted-space"> </span><br>
bfconvert, and the conversion result using Fiji. I am attaching the<span class="m_-8136031225196469418apple-converted-space"> </span><br>
bfconvert log (convert.log)<br>
<convert.log>- Source ND2 file:<span class="m_-8136031225196469418apple-converted-space"> </span><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.biologie.en" target="_blank">https://urldefense.proofpoint.<wbr>com/v2/url?u=https-3A__cloud.<wbr>biologie.en</a><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__s.fr_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=dk4HZH5s6iNWdSqklQk282ZO1Jzo8zFnYNRU3_Sipgk&e=" target="_blank">s.fr</a>_index.php_s_<wbr>H7OPHzLvJ3MPUkd&d=DQIBAg&c=<wbr>j5oPpO0eBH1iio48DtsedbOBGm<br>
uw5jHLjgvtN2r4ehE&r=oU_<wbr>05LztNstAydlbm5L5GDu_<wbr>vAdjXk3frDLx_CqKkuo&m=g6CN<br>
r9rxiOItnhC2oaw8J5mhdFjCF0dh8h<wbr>saIy2xIHw&s=<wbr>tEBqotIUNL7T6mvP82ru7468tzwu<br>
CGWyMTZGnFSM0AY&e=<br>
- Corrupted TIFF generated by bfconvert:<span class="m_-8136031225196469418apple-converted-space"> </span><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.biologie.en" target="_blank">https://urldefense.proofpoint.<wbr>com/v2/url?u=https-3A__cloud.<wbr>biologie.en</a><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__s.fr_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=dk4HZH5s6iNWdSqklQk282ZO1Jzo8zFnYNRU3_Sipgk&e=" target="_blank">s.fr</a>_index.php_s_<wbr>FFOIjHUg6Dl7B1I&d=DQIBAg&c=<wbr>j5oPpO0eBH1iio48DtsedbOBGm<br>
uw5jHLjgvtN2r4ehE&r=oU_<wbr>05LztNstAydlbm5L5GDu_<wbr>vAdjXk3frDLx_CqKkuo&m=g6CN<br>
r9rxiOItnhC2oaw8J5mhdFjCF0dh8h<wbr>saIy2xIHw&s=<wbr>kw3iHYbQD1RC4jD2xAoqzFLatG0n<br>
crEdGR_BdVhwO9o&e=<br>
- Correct TIFF generated by Fiji:<span class="m_-8136031225196469418apple-converted-space"> </span><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.biologie.en" target="_blank">https://urldefense.proofpoint.<wbr>com/v2/url?u=https-3A__cloud.<wbr>biologie.en</a><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__s.fr_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=dk4HZH5s6iNWdSqklQk282ZO1Jzo8zFnYNRU3_Sipgk&e=" target="_blank">s.fr</a>_index.php_s_<wbr>dyl1hZha3pGiP50&d=DQIBAg&c=<wbr>j5oPpO0eBH1iio48DtsedbOBGm<br>
uw5jHLjgvtN2r4ehE&r=oU_<wbr>05LztNstAydlbm5L5GDu_<wbr>vAdjXk3frDLx_CqKkuo&m=g6CN<br>
r9rxiOItnhC2oaw8J5mhdFjCF0dh8h<wbr>saIy2xIHw&s=<wbr>mIZiSrvfdndBpDDckPsYvMtwh98W<br>
_Js7s8ZFy9OMIxg&e=<br>
<br>
Finally, I should mention that at least the latter issue happens with<span class="m_-8136031225196469418apple-converted-space"> </span><br>
files generated with several versions of NIS elements.<br>
<br>
Am I the only person experiencing those issues? Is there any kind of<span class="m_-8136031225196469418apple-converted-space"> </span><br>
additional information I should provide?<br>
<br>
- Version information: bf 5.5.3 and/or Fiji (latest update)<br>
- OS: I encounter the issue on Ubuntu 14.04 and Debian Jessie (8.9)<br>
- java version: I believe the one used is packaged by BioFormats, but<span class="m_-8136031225196469418apple-converted-space"> </span><br>
in case, java -version returns<br>
Ubuntu machine:<br>
java version "1.8.0_144"<br>
Java(TM) SE Runtime Environment (build 1.8.0_144-b01)<br>
Java HotSpot(TM) 64-Bit Server VM (build 25.144-b01, mixed mode)<br>
Debian machine:<br>
java version "1.7.0_131"<br>
OpenJDK Runtime Environment (IcedTea 2.6.9) (7u131-2.6.9-2~deb8u1)<br>
OpenJDK 64-Bit Server VM (build 24.131-b00, mixed mode)<br>
<br>
Thanks a lot!<br>
Maxime<br>
<br>
PS: I tried to upload the files to the QA systemn, but it complains<span class="m_-8136031225196469418apple-converted-space"> </span><br>
that my version of Flash is not up-to-date. I apologize about that and<span class="m_-8136031225196469418apple-converted-space"> </span><br>
hope that you will be able to retrieve the files linked/attached.<br>
PPS: I have checked the "Common issues to check" page before sending<span class="m_-8136031225196469418apple-converted-space"> </span><br>
this email, and I believe that none of them apply.<br>
______________________________<wbr>_________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.<wbr>openmicroscopy.org.uk</a><<a href="mailto:ome-users@lists.openmicro" target="_blank">mailto:<wbr>ome-users@lists.openmicro</a><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__scopy.org.uk_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=CJYCH0Rr1p5e2ZCaJ9nzc02pecGRWBAbMC_aebYK_LU&e=" target="_blank">scopy.org.uk</a>><span class="m_-8136031225196469418apple-converted-space"> </span><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.openmicrosco" target="_blank">https://urldefense.proofpoint.<wbr>com/v2/url?u=http-3A__lists.<wbr>openmicrosco</a><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__py.org.uk_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=2-Mzsn-sJGMlyUWCnDyA1TkprMCwG1fokVV2TVt_lC0&e=" target="_blank">py.org.uk</a>_mailman_listinfo_<wbr>ome-2Dusers&d=DQIBAg&c=<wbr>j5oPpO0eBH1iio48Dtse<br>
dbOBGmuw5jHLjgvtN2r4ehE&r=oU_<wbr>05LztNstAydlbm5L5GDu_<wbr>vAdjXk3frDLx_CqKkuo&<br>
m=<wbr>g6CNr9rxiOItnhC2oaw8J5mhdFjCF0<wbr>dh8hsaIy2xIHw&s=E7dtZPSuF8MP-<wbr>R8RXQ4wOJ<br>
Mw2gRIbrDQO2VivlBdGD8&e=<br>
<br>
<br>
The University of Dundee is a registered Scottish Charity, No:<span class="m_-8136031225196469418apple-converted-space"> </span><br>
SC015096 ______________________________<wbr>_________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.<wbr>openmicroscopy.org.uk</a><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.openmicrosco" target="_blank">https://urldefense.proofpoint.<wbr>com/v2/url?u=http-3A__lists.<wbr>openmicrosco</a><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__py.org.uk_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=2-Mzsn-sJGMlyUWCnDyA1TkprMCwG1fokVV2TVt_lC0&e=" target="_blank">py.org.uk</a>_mailman_listinfo_<wbr>ome-2Dusers&d=DQIBAg&c=<wbr>j5oPpO0eBH1iio48Dtse<br>
dbOBGmuw5jHLjgvtN2r4ehE&r=oU_<wbr>05LztNstAydlbm5L5GDu_<wbr>vAdjXk3frDLx_CqKkuo&<br>
m=<wbr>g6CNr9rxiOItnhC2oaw8J5mhdFjCF0<wbr>dh8hsaIy2xIHw&s=E7dtZPSuF8MP-<wbr>R8RXQ4wOJ<br>
Mw2gRIbrDQO2VivlBdGD8&e=<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif""><br>
<br>
------------------------------<wbr>------------------------------<br>
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution
is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no
liability for any damage caused by any virus transmitted by this email.<br>
==============================<wbr>===<br>
<br>
______________________________<wbr>_________________<br>
ome-users mailing list<br>
</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">ome-users@lists.<wbr>openmicroscopy.org.uk</span></a><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif""><br>
</span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.openmicroscopy.org.uk_mailman_listinfo_ome-2Dusers&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=kivTXoK0uoIWfJkqDoSgyWMIa2-OdMYliaMlKHwHweo&e=" target="_blank"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">http://lists.openmicroscopy.<wbr>org.uk/mailman/listinfo/ome-<wbr>users</span></a><u></u><u></u></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<p class="MsoNormal"><br>
<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
<u></u><u></u></p>
</div></div></div><div><div class="h5">
<p><br>
------------------------------<wbr>------------------------------<br>
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br>
==============================<wbr>===</p></div></div></div>
<br>______________________________<wbr>_________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.<wbr>openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" rel="noreferrer" target="_blank">http://lists.openmicroscopy.<wbr>org.uk/mailman/listinfo/ome-<wbr>users</a><br>
<br></blockquote></div><br></div>