[ome-users] Problem opening .nd2 files, new NIS software version
Sebastien Besson
s.besson at dundee.ac.uk
Thu Sep 5 14:43:24 BST 2013
As a follow-up of this thread,
some recent changes introduced in the Bio-Formats Matlab functions do not
properly work with Matlab versions earlier than R2009b.
A pull request has been opened to fix this function and restore compatibility
with earlier versions:
https://github.com/openmicroscopy/bioformats/pull/688
As part of this change and the ongoing drop of support of Java 1.5, the
current development branches of Bio-Formats will effectively drop support for
Matlab versions earlier than 7.5 (R2007b).
If you currently use Bio-Formats with R2007a or earlier and would not be able
to upgrade Matlab, please let us know so that we can re-evaluate which
versions we support.
Best,
Sebastien
On 4 Sep 2013, at 14:13, Sebastien Besson wrote:
Hi Katrien,
is the following command typed at the Matlab prompt producing the same error:
>> bfGetReader('test.fake');
Which version of the Bio-Formats Matlab functions did you download?
Also which version of Matlab are you running against?
Best,
Sebastien
On 4 Sep 2013, at 09:26, Melissa Linkert wrote:
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<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<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<mailto: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<http://www.biofys.ugent.be/>
[cid:image001.jpg at 01CEA899.F895E9C0]
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Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK Tel: (01382) 386364
The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK Tel: (01382) 386364
The University of Dundee is a registered Scottish Charity, No: SC015096
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