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<div>As a follow-up of this thread, </div>
<div><br>
</div>
<div>some recent changes introduced in the Bio-Formats Matlab functions do not </div>
<div>properly work with Matlab versions earlier than R2009b.</div>
<div>A pull request has been opened to fix this function and restore compatibility </div>
<div>with earlier versions:</div>
<div><a href="https://github.com/openmicroscopy/bioformats/pull/688">https://github.com/openmicroscopy/bioformats/pull/688</a></div>
<div><br>
</div>
<div>As part of this change and the ongoing drop of support of Java 1.5, the </div>
<div>current development branches of Bio-Formats will effectively drop support for </div>
<div>Matlab versions earlier than 7.5 (R2007b).</div>
<div><br>
</div>
<div>If you currently use Bio-Formats with R2007a or earlier and would not be able </div>
<div>to upgrade Matlab, please let us know so that we can re-evaluate which </div>
<div>versions we support.</div>
<div><br>
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br>
</div>
<div>
<div>On 4 Sep 2013, at 14:13, Sebastien Besson wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap:break-word">Hi Katrien,
<div><br>
</div>
<div>is the following command typed at the Matlab prompt producing the same error:</div>
<div>>> bfGetReader('test.fake');</div>
<div><br>
</div>
<div>Which version of the Bio-Formats Matlab functions did you download? </div>
<div>Also which version of Matlab are you running against?</div>
<div><br>
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br>
</div>
<div>
<div>
<div>On 4 Sep 2013, at 09:26, Melissa Linkert wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>Hi Katrien,<br>
<br>
<blockquote type="cite">I tried, but get following error and my image does not open:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">IPS<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">Warning: Concatenation involves an empty array with an incorrect number of rows.<br>
</blockquote>
<blockquote type="cite">This may not be allowed in a future release.<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">In IPSintro at 94<br>
</blockquote>
</blockquote>
<blockquote type="cite"> In IPS at 18<br>
</blockquote>
<blockquote type="cite">??? Error: File: bfGetReader.m Line: 4 Column: 1<br>
</blockquote>
<blockquote type="cite">Unexpected MATLAB operator.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Error in ==> nd2read at 40<br>
</blockquote>
<blockquote type="cite">r = bfGetReader(filepath);<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Error in ==> load_image at 8<br>
</blockquote>
<blockquote type="cite"> bld = nd2read(filepath,locipath);<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Error in ==> ips_load_image at 48<br>
</blockquote>
<blockquote type="cite"> bld = load_image(filepath);<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Error in ==> bldver at 79<br>
</blockquote>
<blockquote type="cite"> ips_load_image(gcbf,filepath)<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">??? Error while evaluating uicontrol Callback<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">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.<br>
</blockquote>
<br>
I'm just forwarding this to the ome-users mailing list; I don't know the<br>
answer off hand, but those on the list with a better understanding of<br>
MATLAB may be able to help.<br>
<br>
Regards,<br>
-Melissa<br>
<br>
On Wed, Sep 04, 2013 at 09:41:11AM +0200, Katrien Forier wrote:<br>
<blockquote type="cite">Dear Melissa,<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">I tried, but get following error and my image does not open:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">IPS<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">Warning: Concatenation involves an empty array with an incorrect number of rows.<br>
</blockquote>
<blockquote type="cite">This may not be allowed in a future release.<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">In IPSintro at 94<br>
</blockquote>
</blockquote>
<blockquote type="cite"> In IPS at 18<br>
</blockquote>
<blockquote type="cite">??? Error: File: bfGetReader.m Line: 4 Column: 1<br>
</blockquote>
<blockquote type="cite">Unexpected MATLAB operator.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Error in ==> nd2read at 40<br>
</blockquote>
<blockquote type="cite">r = bfGetReader(filepath);<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Error in ==> load_image at 8<br>
</blockquote>
<blockquote type="cite"> bld = nd2read(filepath,locipath);<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Error in ==> ips_load_image at 48<br>
</blockquote>
<blockquote type="cite"> bld = load_image(filepath);<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Error in ==> bldver at 79<br>
</blockquote>
<blockquote type="cite"> ips_load_image(gcbf,filepath)<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">??? Error while evaluating uicontrol Callback<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">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.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Kind regards,<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Katrien Forier<br>
</blockquote>
<blockquote type="cite">Pharmacist, PhD student<br>
</blockquote>
<blockquote type="cite">Biophotonic Imaging Group<br>
</blockquote>
<blockquote type="cite">Lab of General Biochemistry and Physical Pharmacy<br>
</blockquote>
<blockquote type="cite">Ghent University<br>
</blockquote>
<blockquote type="cite">Harelbekestraat 72, 9000 Ghent, Belgium<br>
</blockquote>
<blockquote type="cite">Tel: +32 (0)9 264 80 49<br>
</blockquote>
<blockquote type="cite">Fax: +32 (0)9 264 81 89<br>
</blockquote>
<blockquote type="cite">Website: <a href="http://www.biofys.ugent.be/">http://www.biofys.ugent.be</a><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">-----Oorspronkelijk bericht-----<br>
</blockquote>
<blockquote type="cite">Van: Melissa Linkert [mailto:melissa.linkert@gmail.com] Namens Melissa Linkert<br>
</blockquote>
<blockquote type="cite">Verzonden: dinsdag 3 september 2013 17:41<br>
</blockquote>
<blockquote type="cite">Aan: Katrien Forier<br>
</blockquote>
<blockquote type="cite">Onderwerp: Re: [ome-users] Problem opening .nd2 files, new NIS software version<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Hi Katrien,<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">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.<br>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">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:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><a href="https://github.com/openmicroscopy/bioformats/tree/v4.4.8/components/bio-formats/matlab">https://github.com/openmicroscopy/bioformats/tree/v4.4.8/components/bio-formats/matlab</a><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">to your MATLAB path. If you have any further trouble reading files, please let us know on the ome-users list.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Regards,<br>
</blockquote>
<blockquote type="cite">-Melissa<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">On Tue, Sep 03, 2013 at 05:11:49PM +0200, Katrien Forier wrote:<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Hi Melissa,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">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.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Kind regards,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Katrien Forier<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Pharmacist, PhD student<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Biophotonic Imaging Group<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Lab of General Biochemistry and Physical Pharmacy Ghent University
<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Harelbekestraat 72, 9000 Ghent, Belgium<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Tel: +32 (0)9 264 80 49<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Fax: +32 (0)9 264 81 89<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Website: <a href="http://www.biofys.ugent.be/">http://www.biofys.ugent.be</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">-----Oorspronkelijk bericht-----<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Van: Melissa Linkert [mailto:melissa.linkert@gmail.com] Namens Melissa
<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Linkert<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Verzonden: dinsdag 3 september 2013 17:04<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Aan: Katrien Forier<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">CC: <a href="mailto:ome-users@lists.openmicroscopy.org.uk">
ome-users@lists.openmicroscopy.org.uk</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Onderwerp: Re: [ome-users] Problem opening .nd2 files, new NIS
<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">software version<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Hi Katrien,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">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.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">At the moment, I have problems opening .nd2 files obtained using NIS
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Elements Advanced Research version 4.13.04. Using an old <br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci-tools.jar file, I can open files that we obtained with our old
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">NIS version (we were running version 3.10 previously) but not the
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">files obtained using the updated NIS software. Using the latest
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">stable version of loci-tools.jar, I also cannot open any of the
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">files: not the ones we obtained using NIS version 3.1 and not the
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">ones obtained using NIS 4.13.04. I also tried using the trunk build,
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">that just gave me a different error. The errors I get from MatLab
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">are listed below. I also uploaded 2 files to Dropbox (too big for
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">email): one obtained using NIS elements AR 3.1 and one using NIS
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">elements AR4.13.04. I named them OldVersionNIS.nd2 and <br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">NewVersionNIS.nd2 respectively. You can find them here:<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><a href="https://www.dropbox.com/sh/jxyl7ahiruv2lh3/PoWsdLdPtg">https://www.dropbox.com/sh/jxyl7ahiruv2lh3/PoWsdLdPtg</a><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">It would be nice if we could open both files again in our software.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Please let me know if you need any further information.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Thank you for the report, and for providing sample files.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Here is the error I get when running our old loci-tools.jar on a file obtained using the latest version of NIS:<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">??? Java exception occurred:<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">java.lang.ArithmeticException: / by zero<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.in.ND2Reader.initFile(ND2Reader.java:379)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.FormatReader.setId(FormatReader.java:214)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.ImageReader.setId(ImageReader.java:573)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.ReaderWrapper.setId(ReaderWrapper.java:75)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.ChannelFiller.setId(ChannelFiller.java:186)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.ReaderWrapper.setId(ReaderWrapper.java:75)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.ChannelSeparator.setId(ChannelSeparator.java:61)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> nd2read at 42<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">r.setId(filepath);<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> load_image at 8<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> bld = nd2read(filepath,locipath);<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> ips_load_image at 48<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> bld = load_image(filepath);<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> bldver at 79<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> ips_load_image(gcbf,filepath)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">??? Error while evaluating uicontrol Callback<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">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.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">And here is the error I get when I repeat it, buit with the trunk build loci-tools.jar file:<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">log4j:WARN No appenders could be found for logger (ome.scifio.io.NIOByteBufferProvider).<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">log4j:WARN Please initialize the log4j system properly.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">??? No appropriate method or public field openImage for class loci.formats.ChannelSeparator.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> nd2read at 78<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> img = r.openImage(i - 1);<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> load_image at 8<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> bld = nd2read(filepath,locipath);<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> ips_load_image at 48<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> bld = load_image(filepath);<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> bldver at 79<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> ips_load_image(gcbf,filepath)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">??? Error while evaluating uicontrol Callback<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">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:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><a href="http://www.openmicroscopy.org/site/support/bio-formats4/users/matlab/i">http://www.openmicroscopy.org/site/support/bio-formats4/users/matlab/i</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">ndex.html <br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><a href="http://www.openmicroscopy.org/site/support/bio-formats4/developers/mat">http://www.openmicroscopy.org/site/support/bio-formats4/developers/mat</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">lab-dev.html<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">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.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Regards,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">-Melissa<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">On Tue, Sep 03, 2013 at 11:56:55AM +0200, Katrien Forier wrote:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Dear Sir or Madam,<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">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.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">At the moment, I have problems opening .nd2 files obtained using NIS
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Elements Advanced Research version 4.13.04. Using an old <br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci-tools.jar file, I can open files that we obtained with our old
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">NIS version (we were running version 3.10 previously) but not the
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">files obtained using the updated NIS software. Using the latest
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">stable version of loci-tools.jar, I also cannot open any of the
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">files: not the ones we obtained using NIS version 3.1 and not the
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">ones obtained using NIS 4.13.04. I also tried using the trunk build,
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">that just gave me a different error. The errors I get from MatLab
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">are listed below. I also uploaded 2 files to Dropbox (too big for
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">email): one obtained using NIS elements AR 3.1 and one using NIS
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">elements AR4.13.04. I named them OldVersionNIS.nd2 and <br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">NewVersionNIS.nd2 respectively. You can find them here:<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><a href="https://www.dropbox.com/sh/jxyl7ahiruv2lh3/PoWsdLdPtg">https://www.dropbox.com/sh/jxyl7ahiruv2lh3/PoWsdLdPtg</a><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">It would be nice if we could open both files again in our software.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Please let me know if you need any further information.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Here is the error I get when running our old loci-tools.jar on a file obtained using the latest version of NIS:<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">??? Java exception occurred:<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">java.lang.ArithmeticException: / by zero<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.in.ND2Reader.initFile(ND2Reader.java:379)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.FormatReader.setId(FormatReader.java:214)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.ImageReader.setId(ImageReader.java:573)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.ReaderWrapper.setId(ReaderWrapper.java:75)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.ChannelFiller.setId(ChannelFiller.java:186)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.ReaderWrapper.setId(ReaderWrapper.java:75)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> at<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">loci.formats.ChannelSeparator.setId(ChannelSeparator.java:61)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> nd2read at 42<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">r.setId(filepath);<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> load_image at 8<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> bld = nd2read(filepath,locipath);<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> ips_load_image at 48<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> bld = load_image(filepath);<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> bldver at 79<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> ips_load_image(gcbf,filepath)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">??? Error while evaluating uicontrol Callback<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">And here is the error I get when I repeat it, buit with the trunk build loci-tools.jar file:<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">log4j:WARN No appenders could be found for logger (ome.scifio.io.NIOByteBufferProvider).<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">log4j:WARN Please initialize the log4j system properly.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">??? No appropriate method or public field openImage for class loci.formats.ChannelSeparator.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> nd2read at 78<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> img = r.openImage(i - 1);<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> load_image at 8<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> bld = nd2read(filepath,locipath);<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> ips_load_image at 48<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> bld = load_image(filepath);<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Error in ==> bldver at 79<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"> ips_load_image(gcbf,filepath)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">??? Error while evaluating uicontrol Callback<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Kind regards,<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Katrien Forier<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Pharmacist, PhD student<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Biophotonic Imaging Group<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Lab of General Biochemistry and Physical Pharmacy Ghent University
<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Harelbekestraat 72, 9000 Ghent, Belgium<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Tel: +32 (0)9 264 80 49<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Fax: +32 (0)9 264 81 89<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Website: <a href="http://www.biofys.ugent.be/">http://www.biofys.ugent.be</a><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">[cid:image001.jpg@01CEA899.F895E9C0]<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">_______________________________________________<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">ome-users mailing list<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br>
</div>
</blockquote>
</div>
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<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
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<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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<div style="word-wrap:break-word">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
</div>
</span></div>
</span></span></div>
<br>
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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