[ome-users] Problem opening .nd2 files, new NIS software version
Melissa Linkert
melissa at glencoesoftware.com
Tue Sep 3 16:03:52 BST 2013
Hi Katrien,
> We use an in house developed software package to analyze .nd2 files. Our software in integrated in MatLab and we use the loci-tools.jar to be able to open the files.
> At the moment, I have problems opening .nd2 files obtained using NIS Elements Advanced Research version 4.13.04. Using an old loci-tools.jar file, I can open files that we obtained with our old NIS version (we were running version 3.10 previously) but not the files obtained using the updated NIS software. Using the latest stable version of loci-tools.jar, I also cannot open any of the files: not the ones we obtained using NIS version 3.1 and not the ones obtained using NIS 4.13.04. I also tried using the trunk build, that just gave me a different error. The errors I get from MatLab are listed below. I also uploaded 2 files to Dropbox (too big for email): one obtained using NIS elements AR 3.1 and one using NIS elements AR4.13.04. I named them OldVersionNIS.nd2 and NewVersionNIS.nd2 respectively. You can find them here: https://www.dropbox.com/sh/jxyl7ahiruv2lh3/PoWsdLdPtg
> It would be nice if we could open both files again in our software.
>
> Please let me know if you need any further information.
Thank you for the report, and for providing sample files.
> Here is the error I get when running our old loci-tools.jar on a file obtained using the latest version of NIS:
>
> ??? Java exception occurred:
> java.lang.ArithmeticException: / by zero
>
> at loci.formats.in.ND2Reader.initFile(ND2Reader.java:379)
>
> at loci.formats.FormatReader.setId(FormatReader.java:214)
>
> at loci.formats.ImageReader.setId(ImageReader.java:573)
>
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:75)
>
> at loci.formats.ChannelFiller.setId(ChannelFiller.java:186)
>
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:75)
>
> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:61)
>
>
> Error in ==> nd2read at 42
> r.setId(filepath);
>
> Error in ==> load_image at 8
> bld = nd2read(filepath,locipath);
>
> Error in ==> ips_load_image at 48
> bld = load_image(filepath);
>
> Error in ==> bldver at 79
> ips_load_image(gcbf,filepath)
>
> ??? Error while evaluating uicontrol Callback
Do you know which version of Bio-Formats is being used here? From
initial debugging, it looks like the version being used is several years
old.
> And here is the error I get when I repeat it, buit with the trunk build loci-tools.jar file:
>
>
> log4j:WARN No appenders could be found for logger (ome.scifio.io.NIOByteBufferProvider).
> log4j:WARN Please initialize the log4j system properly.
> ??? No appropriate method or public field openImage for class loci.formats.ChannelSeparator.
>
> Error in ==> nd2read at 78
> img = r.openImage(i - 1);
>
> Error in ==> load_image at 8
> bld = nd2read(filepath,locipath);
>
> Error in ==> ips_load_image at 48
> bld = load_image(filepath);
>
> Error in ==> bldver at 79
> ips_load_image(gcbf,filepath)
>
> ??? Error while evaluating uicontrol Callback
This error means that nd2read.m is attempting to use a function in
Bio-Formats that no longer exists. Could you please send the complete
contents of nd2read.m and load_image.m? If we have those files, then we
can suggest how best to update them to work with newer versions of
Bio-Formats. You may also want to have a look at the Matlab pages on
the Bio-Formats website for information about how to use recent versions
of Bio-Formats with Matlab:
http://www.openmicroscopy.org/site/support/bio-formats4/users/matlab/index.html
http://www.openmicroscopy.org/site/support/bio-formats4/developers/matlab-dev.html
We were able to confirm that both files can be opened with the current
stable version (4.4.8) and the current trunk build, so hopefully some
minor updates to your existing .m files will allow everything to work
again.
Regards,
-Melissa
On Tue, Sep 03, 2013 at 11:56:55AM +0200, Katrien Forier wrote:
> Dear Sir or Madam,
>
> We use an in house developed software package to analyze .nd2 files. Our software in integrated in MatLab and we use the loci-tools.jar to be able to open the files.
> At the moment, I have problems opening .nd2 files obtained using NIS Elements Advanced Research version 4.13.04. Using an old loci-tools.jar file, I can open files that we obtained with our old NIS version (we were running version 3.10 previously) but not the files obtained using the updated NIS software. Using the latest stable version of loci-tools.jar, I also cannot open any of the files: not the ones we obtained using NIS version 3.1 and not the ones obtained using NIS 4.13.04. I also tried using the trunk build, that just gave me a different error. The errors I get from MatLab are listed below. I also uploaded 2 files to Dropbox (too big for email): one obtained using NIS elements AR 3.1 and one using NIS elements AR4.13.04. I named them OldVersionNIS.nd2 and NewVersionNIS.nd2 respectively. You can find them here: https://www.dropbox.com/sh/jxyl7ahiruv2lh3/PoWsdLdPtg
> It would be nice if we could open both files again in our software.
>
> Please let me know if you need any further information.
>
> Here is the error I get when running our old loci-tools.jar on a file obtained using the latest version of NIS:
>
> ??? Java exception occurred:
> java.lang.ArithmeticException: / by zero
>
> at loci.formats.in.ND2Reader.initFile(ND2Reader.java:379)
>
> at loci.formats.FormatReader.setId(FormatReader.java:214)
>
> at loci.formats.ImageReader.setId(ImageReader.java:573)
>
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:75)
>
> at loci.formats.ChannelFiller.setId(ChannelFiller.java:186)
>
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:75)
>
> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:61)
>
>
> Error in ==> nd2read at 42
> r.setId(filepath);
>
> Error in ==> load_image at 8
> bld = nd2read(filepath,locipath);
>
> Error in ==> ips_load_image at 48
> bld = load_image(filepath);
>
> Error in ==> bldver at 79
> ips_load_image(gcbf,filepath)
>
> ??? Error while evaluating uicontrol Callback
>
>
> And here is the error I get when I repeat it, buit with the trunk build loci-tools.jar file:
>
>
> log4j:WARN No appenders could be found for logger (ome.scifio.io.NIOByteBufferProvider).
> log4j:WARN Please initialize the log4j system properly.
> ??? No appropriate method or public field openImage for class loci.formats.ChannelSeparator.
>
> Error in ==> nd2read at 78
> img = r.openImage(i - 1);
>
> Error in ==> load_image at 8
> bld = nd2read(filepath,locipath);
>
> Error in ==> ips_load_image at 48
> bld = load_image(filepath);
>
> Error in ==> bldver at 79
> ips_load_image(gcbf,filepath)
>
> ??? Error while evaluating uicontrol Callback
>
>
> Kind regards,
>
> Katrien Forier
> Pharmacist, PhD student
> Biophotonic Imaging Group
> Lab of General Biochemistry and Physical Pharmacy
> Ghent University
> Harelbekestraat 72, 9000 Ghent, Belgium
> Tel: +32 (0)9 264 80 49
> Fax: +32 (0)9 264 81 89
> Website: http://www.biofys.ugent.be
>
> [cid:image001.jpg at 01CEA899.F895E9C0]
>
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