[ome-users] Problem opening .nd2 files, new NIS software version
Melissa Linkert
melissa at glencoesoftware.com
Wed Sep 4 09:26:07 BST 2013
Hi Katrien,
> I tried, but get following error and my image does not open:
>
> >> IPS
> Warning: Concatenation involves an empty array with an incorrect number of rows.
> This may not be allowed in a future release.
> > In IPSintro at 94
> In IPS at 18
> ??? Error: File: bfGetReader.m Line: 4 Column: 1
> Unexpected MATLAB operator.
>
> Error in ==> nd2read at 40
> r = bfGetReader(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
>
> >>
>
> Could you please walk me through the steps of fixing this? I'm really no MATLAB expert, so a step by step explanation could be useful.
I'm just forwarding this to the ome-users mailing list; I don't know the
answer off hand, but those on the list with a better understanding of
MATLAB may be able to help.
Regards,
-Melissa
On Wed, Sep 04, 2013 at 09:41:11AM +0200, Katrien Forier wrote:
> Dear Melissa,
>
> I tried, but get following error and my image does not open:
>
> >> IPS
> Warning: Concatenation involves an empty array with an incorrect number of rows.
> This may not be allowed in a future release.
> > In IPSintro at 94
> In IPS at 18
> ??? Error: File: bfGetReader.m Line: 4 Column: 1
> Unexpected MATLAB operator.
>
> Error in ==> nd2read at 40
> r = bfGetReader(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
>
> >>
>
> Could you please walk me through the steps of fixing this? I'm really no MATLAB expert, so a step by step explanation could be useful.
>
> 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
>
>
> -----Oorspronkelijk bericht-----
> Van: Melissa Linkert [mailto:melissa.linkert at gmail.com] Namens Melissa Linkert
> Verzonden: dinsdag 3 september 2013 17:41
> Aan: Katrien Forier
> Onderwerp: Re: [ome-users] Problem opening .nd2 files, new NIS software version
>
> Hi Katrien,
>
> > Thank you very much for your help. I do not know how old the old plugin is. Several years is possible, yes. I included the files you requested in the attachment and look forward to your suggestions.
>
> Thank you for sending the .m files. After discussing with our MATLAB team, the attached updated nd2read.m should work with recent versions of Bio-Formats. You will also need to add the bfGetReader.m and bfGetPlane.m from:
>
> https://github.com/openmicroscopy/bioformats/tree/v4.4.8/components/bio-formats/matlab
>
> to your MATLAB path. If you have any further trouble reading files, please let us know on the ome-users list.
>
> Regards,
> -Melissa
>
> On Tue, Sep 03, 2013 at 05:11:49PM +0200, Katrien Forier wrote:
> > Hi Melissa,
> >
> > Thank you very much for your help. I do not know how old the old plugin is. Several years is possible, yes. I included the files you requested in the attachment and look forward to your suggestions.
> >
> > 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
> >
> >
> > -----Oorspronkelijk bericht-----
> > Van: Melissa Linkert [mailto:melissa.linkert at gmail.com] Namens Melissa
> > Linkert
> > Verzonden: dinsdag 3 september 2013 17:04
> > Aan: Katrien Forier
> > CC: ome-users at lists.openmicroscopy.org.uk
> > Onderwerp: Re: [ome-users] Problem opening .nd2 files, new NIS
> > software version
> >
> > 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/i
> > ndex.html
> > http://www.openmicroscopy.org/site/support/bio-formats4/developers/mat
> > lab-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]
> > >
> >
> >
> >
> > > _______________________________________________
> > > ome-users mailing list
> > > ome-users at lists.openmicroscopy.org.uk
> > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
>
>
>
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