[ome-users] Problem opening .nd2 files, new NIS software version

[Katrien Forier]

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

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