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Hi Kouichi,
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<div class="">We have been trying to reproduce this issue with the sample file you provided. After testing across different platforms and versions we have so far been unable to do so.</div>
<div class="">What would be helpful for our investigation would be to find out exactly where the J2K classes are being loaded from in MATLAB.</div>
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<div class="">This can be done by creating a MATLAB function 'whereisjavaclassloadingfrom’ which can be found at this link <a href="https://github.com/dgault/bioformats/blob/a75a1f84a389a395529a876fed38b1ed384b88fb/components/formats-gpl/matlab/whereisjavaclassloadingfrom.m" class="">https://github.com/dgault/bioformats/blob/a75a1f84a389a395529a876fed38b1ed384b88fb/components/formats-gpl/matlab/whereisjavaclassloadingfrom.m</a></div>
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<div class="">This can then be run with the following commands to find the version and location of the class:</div>
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<div class=""><font color="#0056d6" class=""><span class="Apple-tab-span" style="white-space: pre;"></span>whereisjavaclassloadingfrom('com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader')</font></div>
<div class=""><font color="#0056d6" class=""><span class="Apple-tab-span" style="white-space: pre;"></span>whereisjavaclassloadingfrom('com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState’)</font></div>
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<div class="">This should output<font color="#0056d6" class=""> </font>results similar to below:</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Version: 9.3.0.713579 (R2017b)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Class: com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>ClassLoader: sun.misc.Launcher$AppClassLoader@c387f44</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>URL: jar:file:/path/to/bioformats_package.jar!/com/sun/media/imageioimpl/plugins/jpeg2000/J2KImageReader.class</div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<div class="">On 25 Oct 2017, at 23:30, Kouichi C. Nakamura <<a href="mailto:kouichi.c.nakamura@gmail.com" class="">kouichi.c.nakamura@gmail.com</a>> wrote:</div>
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<p class="">Hi David,</p>
<p class="">I tried deployment of javaclassoath.txt to the folder, but I got a warning and then error message.</p>
<p class="">Best, <br class="">
</p>
<p class="">Kouichi<br class="">
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<div class="diagnosticMessage-messagePart">Warning: "bioformats_package.jar" is already specified on static java path.</div>
<pre class="">Reading series #1
</pre>
<div class="diagnosticMessage-messagePart">Error using <a href="matlab:matlab.internal.language.introspective.errorDocCallback%28%27bfGetPlane%27,%20%27D:%5CDropbox%5CPrivate_Dropbox%5Cmatlab_toolbox%5Cbfmatlab%5CbfGetPlane.m%27,%2078%29" style="font-weight:bold" class="">
bfGetPlane</a> (<a href="matlab:%20opentoline%28%27D:%5CDropbox%5CPrivate_Dropbox%5Cmatlab_toolbox%5Cbfmatlab%5CbfGetPlane.m%27,78,0%29" class="">line 78</a>)<br class="">
Java exception occurred: <br class="">
java.lang.RuntimeException: jj2000.j2k.fileformat.reader.FileFormatReader.<init>(Ljj2000/j2k/io/RandomAccessIO;Lcom/sun/media/imageioimpl/plugins/jpeg2000/J2KMetadata;)V<br class="">
at com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.initializeRead(J2KReadState.java:729)<br class="">
at com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.<init>(J2KReadState.java:241)<br class="">
at com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader.readRaster(J2KImageReader.java:551)<br class="">
at ome.codecs.services.JAIIIOServiceImpl.readRaster(JAIIIOServiceImpl.java:177)<br class="">
at ome.codecs.JPEG2000Codec.decompress(JPEG2000Codec.java:296) <br class="">
at ome.codecs.JPEG2000Codec.decompress(JPEG2000Codec.java:267) <br class="">
at loci.formats.codec.WrappedCodec.decompress(WrappedCodec.java:132) <br class="">
at loci.formats.codec.JPEG2000Codec.decompress(JPEG2000Codec.java:63) <br class="">
at loci.formats.in.JPEG2000Reader.openBytes(JPEG2000Reader.java:182) <br class="">
at loci.formats.ImageReader.openBytes(ImageReader.java:457) <br class="">
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156) <br class="">
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:148) <br class="">
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) <br class="">
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:159) <br class="">
Caused by: java.lang.NoSuchMethodError: jj2000.j2k.fileformat.reader.FileFormatReader.<init>(Ljj2000/j2k/io/RandomAccessIO;Lcom/sun/media/imageioimpl/plugins/jpeg2000/J2KMetadata;)V<br class="">
at com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.initializeRead(J2KReadState.java:450)<br class="">
... 13 more <br class="">
Error in <a href="matlab:matlab.internal.language.introspective.errorDocCallback%28%27bfopen%27,%20%27D:%5CDropbox%5CPrivate_Dropbox%5Cmatlab_toolbox%5Cbfmatlab%5Cbfopen.m%27,%20150%29" style="font-weight:bold" class="">
bfopen</a> (<a href="matlab:%20opentoline%28%27D:%5CDropbox%5CPrivate_Dropbox%5Cmatlab_toolbox%5Cbfmatlab%5Cbfopen.m%27,150,0%29" class="">line 150</a>)<br class="">
arr = bfGetPlane(r, i, varargin{:});</div>
<pre class=""> .</pre>
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