[ome-users] [Software Feedback] LOCI error message
Melissa Linkert
melissa at glencoesoftware.com
Wed Apr 3 14:28:50 BST 2013
Hi Ye,
> > 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.
We have a fix for this problem under review, and expect to have a
development build with the fix available in the next one to two weeks.
Regards,
-Melissa
On Mon, Apr 01, 2013 at 01:29:42PM -0500, Curtis Rueden wrote:
> Hi Ye,
>
> > 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.
>
> Apologies for the delay; I have been out sick the past few days. 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.
>
> Regards,
> Curtis
>
>
> On Tue, Mar 26, 2013 at 11:32 PM, Ye Chen <yechen at swin.edu.au> wrote:
>
> > HI Curtis,****
> >
> > ** **
> >
> > 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 could open
> > the problematic nd2 files with NIKON’s reade, but it does not allow me to
> > save as a tiff stack…****
> >
> > ** **
> >
> > Best regards,****
> >
> > ** **
> >
> > Ye****
> >
> > ** **
> >
> > *From:* ctrueden.wisc at gmail.com [mailto:ctrueden.wisc at gmail.com] *On
> > Behalf Of *Curtis Rueden
> > *Sent:* Friday, 22 March 2013 4:34 AM
> > *To:* Ye Chen
> > *Cc:* OME-users mailing list
> >
> > *Subject:* Re: [Software Feedback] LOCI error message****
> >
> > ** **
> >
> > Hi Ye,****
> >
> > ** **
> >
> > > I have uploaded the file under the name “LOCI_YECHEN_Swinburne.nd2”.****
> >
> > ** **
> >
> > 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.****
> >
> > ** **
> >
> > Regards,****
> >
> > Curtis****
> >
> > ** **
> >
> > On Wed, Mar 20, 2013 at 4:36 PM, Ye Chen <yechen at swin.edu.au> wrote:****
> >
> > Hi Curtis,****
> >
> > ****
> >
> > Thank you for your help. I have uploaded the file under the name
> > “LOCI_YECHEN_Swinburne.nd2”. ****
> >
> > ****
> >
> > 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.****
> >
> > ****
> >
> > 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.****
> >
> > ****
> >
> > I hope those information will help somehow and I really appreciate your
> > help.****
> >
> > ****
> >
> > Best regards,****
> >
> > ****
> >
> > Ye****
> >
> > ****
> >
> > ****
> >
> > Ye Chen, Ph.D. H34****
> >
> > Centre for Micro-Photonics****
> >
> > Faculty of Engineering and Industrial Sciences****
> >
> > Swinburne University of Technology****
> >
> > 1 Alfred St. Hawthorn****
> >
> > Victoria 3122, Australia****
> >
> > (CRICOS Provider 00111D)****
> >
> > Ph +61-3-9214-5649****
> >
> > ****
> >
> > ****
> >
> > ****
> >
> > *From:* ctrueden.wisc at gmail.com [mailto:ctrueden.wisc at gmail.com] *On
> > Behalf Of *Curtis Rueden
> > *Sent:* Wednesday, 20 March 2013 5:14 AM
> > *To:* Ye Chen
> > *Cc:* bf at openmicroscopy.org.uk
> > *Subject:* Re: [Software Feedback] LOCI error message****
> >
> > ****
> >
> > Hi Ye,****
> >
> > ****
> >
> > > Could you please provide me a FTP address to upload the nd2 file,****
> >
> > > since the smallest one is ~600M?****
> >
> > ****
> >
> > Here are the credentials for our SFTP server:****
> >
> > ****
> >
> > server: dev.loci.wisc.edu****
> >
> > port: 22****
> >
> > user: ftpuser****
> >
> > pass: badgerbioformats~****
> >
> > ****
> >
> > Please let us know if/when you have uploaded any data there.****
> >
> > ****
> >
> > Thanks,****
> >
> > Curtis****
> >
> > ****
> >
> > On Sun, Mar 17, 2013 at 12:25 AM, <yechen at swin.edu.au> wrote:****
> >
> > Ye Chen sent a message using the contact form at
> > http://loci.wisc.edu/contact.
> >
> > Hi,
> >
> > 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?
> >
> > Best regards,
> >
> > Ye
> >
> > Ye Chen, Ph.D. H34
> > Centre for Micro-Photonics
> > Faculty of Engineering and Industrial Sciences
> > Swinburne University of Technology
> > 1 Alfred St. Hawthorn
> > Victoria 3122, Australia
> > (CRICOS Provider 00111D)
> > Ph +61-3-9214-5649
> >
> >
> > java.lang.StringIndexOutOfBoundsException: String index out of
> > range: -9
> >
> > at java.lang.String.substring(String.java:1937)
> >
> > at loci.formats.in
> > .NativeND2Reader.initFile(NativeND2Reader.java:490)
> >
> > at loci.formats.FormatReader.setId(FormatReader.java:1178)
> >
> > at loci.formats.DelegateReader.setId(DelegateReader.java:259)
> >
> > at
> > loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
> >
> > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
> >
> > at loci.plugins.in.Importer.showDialogs(Importer.java:141)
> >
> > at loci.plugins.in.Importer.run(Importer.java:79)
> >
> > at loci.plugins.LociImporter.run(LociImporter.java:81)
> >
> > at ij.IJ.runUserPlugIn(IJ.java:183)
> >
> > at ij.IJ.runPlugIn(IJ.java:150)
> >
> > at ij.Executer.runCommand(Executer.java:127)
> >
> > at ij.Executer.run(Executer.java:64)
> >
> > at ij.IJ.run(IJ.java:249)
> >
> > at ij.IJ.run(IJ.java:227)
> >
> > at ij.macro.Functions.doRun(Functions.java:581)
> >
> > at ij.macro.Functions.doFunction(Functions.java:82)
> >
> > at ij.macro.Interpreter.doStatement(Interpreter.java:203)
> >
> > at ij.macro.Interpreter.doBlock(Interpreter.java:526)
> >
> > at ij.macro.Interpreter.runMacro(Interpreter.java:130)
> >
> > at ij.macro.MacroRunner.run(MacroRunner.java:143)
> >
> > at java.lang.Thread.run(Thread.java:619)****
> >
> > ****
> >
> > ** **
> >
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