<div dir="ltr">Hi Ye,<div><br></div><div><div>> If you could let me know normally how long it takes to fix such a</div><div>> problem. If it is a couple of weeks, I can wait. Otherwise I will try</div><div>> to work around this problem using other methods.</div>
</div><div><br></div><div>Apologies for the delay; I have been out sick the past few days. <span style="font-size:13px;font-family:arial,sans-serif">Once again I am CCing the OME-users list, since other OME developers are better equipped to comment on the expected length of time for bugfixes.</span><br>
</div><div style><br></div><div><span style="font-family:arial,sans-serif;font-size:13px">Regards,</span></div><div><span style="font-family:arial,sans-serif;font-size:13px">Curtis</span></div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Tue, Mar 26, 2013 at 11:32 PM, Ye Chen <span dir="ltr"><<a href="mailto:yechen@swin.edu.au" target="_blank">yechen@swin.edu.au</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-AU" link="blue" vlink="purple">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">HI Curtis,<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">Thank you again for your help. I am by no means pushing you or your group. If you could let me know normally how long it takes to fix such a problem. If it
is a couple of weeks, I can wait. Otherwise I will try to work around this problem using other methods. Today I went through the OME email list, it seems to be a common issue after NIS4 update in NIKON.
<i> </i>I could open the problematic nd2 files with NIKON’s reade, but it does not allow me to save as a tiff stack…<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">Best regards,<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">Ye<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"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:ctrueden.wisc@gmail.com" target="_blank">ctrueden.wisc@gmail.com</a> [mailto:<a href="mailto:ctrueden.wisc@gmail.com" target="_blank">ctrueden.wisc@gmail.com</a>]
<b>On Behalf Of </b>Curtis Rueden<br>
<b>Sent:</b> Friday, 22 March 2013 4:34 AM<br>
<b>To:</b> Ye Chen<br>
<b>Cc:</b> OME-users mailing list</span></p><div><div class="h5"><br>
<b>Subject:</b> Re: [Software Feedback] LOCI error message<u></u><u></u></div></div><p></p><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">Hi Ye,<u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<div>
<p class="MsoNormal">> I have uploaded the file under the name “LOCI_YECHEN_Swinburne.nd2”.<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Thank you! Once again I am CCing the OME-users list to keep the OME team involved in the discussion. We will investigate the issue and reply back with our findings.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Regards,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Curtis<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><u></u> <u></u></p>
<div>
<p class="MsoNormal">On Wed, Mar 20, 2013 at 4:36 PM, Ye Chen <<a href="mailto:yechen@swin.edu.au" target="_blank">yechen@swin.edu.au</a>> wrote:<u></u><u></u></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hi Curtis,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thank you for your help. I have uploaded the file under the name “LOCI_YECHEN_Swinburne.nd2”.
</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Let me explain a bit more. I acquired those kinds of file for STORM imaging (a type of super-resolution
imaging). The way NIKON implement it is nothing specially but in their ‘5D’ mode, which acquire a stack of live images that may have alternative lasers for different frame. But in the file I send you, there is no changes of laser.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">This problem often arises when I terminate the experiment earlier. Say, I set the experiment to be
40k frames but decided to stop at 20k. There had been no problem for LOCI to import this type of files until last month. Interestingly, I have not updated the NIKON software nor the LOCI or imageJ for a long time, which makes the problem more puzzling. Nevertheless,
even sometime, for an experiment that ended normally, that is to say it ran to 40k frames, the file can’t be opened properly.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I hope those information will help somehow and I really appreciate your help.</span><u></u><u></u></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Best regards,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Ye</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:12.0pt">
<span style="color:#1f497d">Ye Chen, Ph.D. H34</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:12.0pt">
<span style="color:#1f497d">Centre for Micro-Photonics</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:12.0pt">
<span style="color:#1f497d">Faculty of Engineering and Industrial Sciences</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:12.0pt">
<span style="color:#1f497d">Swinburne University of Technology</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:12.0pt">
<span style="color:#1f497d">1 Alfred St. Hawthorn</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:12.0pt">
<span style="color:#1f497d">Victoria 3122, Australia</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:12.0pt">
<span style="color:#1f497d">(CRICOS Provider 00111D)</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:12.0pt">
<span style="color:#1f497d">Ph <a href="tel:%2B61-3-9214-5649" target="_blank">+61-3-9214-5649</a></span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
</div>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a href="mailto:ctrueden.wisc@gmail.com" target="_blank">ctrueden.wisc@gmail.com</a> [mailto:<a href="mailto:ctrueden.wisc@gmail.com" target="_blank">ctrueden.wisc@gmail.com</a>]
<b>On Behalf Of </b>Curtis Rueden<br>
<b>Sent:</b> Wednesday, 20 March 2013 5:14 AM<br>
<b>To:</b> Ye Chen<br>
<b>Cc:</b> <a href="mailto:bf@openmicroscopy.org.uk" target="_blank">bf@openmicroscopy.org.uk</a><br>
<b>Subject:</b> Re: [Software Feedback] LOCI error message</span><u></u><u></u></p>
<div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">Hi Ye,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">> Could you please provide me a FTP address to upload the nd2 file,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">> since the smallest one is ~600M?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Here are the credentials for our SFTP server:<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">server:
<a href="http://dev.loci.wisc.edu" target="_blank">dev.loci.wisc.edu</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">port: 22<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">user: ftpuser<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">pass: badgerbioformats~<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Please let us know if/when you have uploaded any data there.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Thanks,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Curtis<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"> <u></u><u></u></p>
<div>
<p class="MsoNormal">On Sun, Mar 17, 2013 at 12:25 AM, <<a href="mailto:yechen@swin.edu.au" target="_blank">yechen@swin.edu.au</a>> wrote:<u></u><u></u></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Ye Chen sent a message using the contact form at
<a href="http://loci.wisc.edu/contact" target="_blank">http://loci.wisc.edu/contact</a>.<br>
<br>
Hi,<br>
<br>
I got the following error message from LOCI while loading several NIKON .nd2 files. This happened with many files and trunk/lateast/stable version of LOCI, so that I hope you could help me sorting out the reason. My ImageJ (64-bit) is running on win-7 64-bit
system. Could you please provide me a FTP address to upload the nd2 file, since the smallest one is ~600M?<br>
<br>
Best regards,<br>
<br>
Ye<br>
<br>
Ye Chen, Ph.D. H34<br>
Centre for Micro-Photonics<br>
Faculty of Engineering and Industrial Sciences<br>
Swinburne University of Technology<br>
1 Alfred St. Hawthorn<br>
Victoria 3122, Australia<br>
(CRICOS Provider 00111D)<br>
Ph <a href="tel:%2B61-3-9214-5649" target="_blank">+61-3-9214-5649</a><br>
<br>
<br>
java.lang.StringIndexOutOfBoundsException: String index out of range: -9<br>
<br>
at java.lang.String.substring(String.java:1937)<br>
<br>
at <a href="http://loci.formats.in" target="_blank">loci.formats.in</a>.NativeND2Reader.initFile(NativeND2Reader.java:490)<br>
<br>
at loci.formats.FormatReader.setId(FormatReader.java:1178)<br>
<br>
at loci.formats.DelegateReader.setId(DelegateReader.java:259)<br>
<br>
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)<br>
<br>
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)<br>
<br>
at loci.plugins.in.Importer.showDialogs(Importer.java:141)<br>
<br>
at loci.plugins.in.Importer.run(Importer.java:79)<br>
<br>
at loci.plugins.LociImporter.run(LociImporter.java:81)<br>
<br>
at ij.IJ.runUserPlugIn(IJ.java:183)<br>
<br>
at ij.IJ.runPlugIn(IJ.java:150)<br>
<br>
at ij.Executer.runCommand(Executer.java:127)<br>
<br>
at ij.Executer.run(Executer.java:64)<br>
<br>
at ij.IJ.run(IJ.java:249)<br>
<br>
at ij.IJ.run(IJ.java:227)<br>
<br>
at ij.macro.Functions.doRun(Functions.java:581)<br>
<br>
at ij.macro.Functions.doFunction(Functions.java:82)<br>
<br>
at ij.macro.Interpreter.doStatement(Interpreter.java:203)<br>
<br>
at ij.macro.Interpreter.doBlock(Interpreter.java:526)<br>
<br>
at ij.macro.Interpreter.runMacro(Interpreter.java:130)<br>
<br>
at ij.macro.MacroRunner.run(MacroRunner.java:143)<br>
<br>
at java.lang.Thread.run(Thread.java:619)<u></u><u></u></p>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
</div>
</div></div></div>
</div>
</blockquote></div><br></div>