[ome-users] [Software Feedback] LOCI error message

Mon Apr 1 19:29:42 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.

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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