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<div class="">Hi,</div>
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<div class="">Thanks for the additional information and notably including the MATLAB/Java version.</div>
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<div class="">Bio-Formats 6.0.0 bumps the minimal supported Java version to 8 [1]. For MATLAB users, this means it is no longer possible to use old versions of MATLAB shipping JVM 7 natively with Bio-Formats 6. There are two possibilities:</div>
<div class=""><br class="">
</div>
<div class="">- if possible, upgrading to MATLAB R2017b or later is recommended. R2017b is the first version which ships an embedded version of Java 8 [2]</div>
<div class="">- if upgrading is not a possibility, it should be possible to point MATLAB at a different JVM than the embedded one [3].</div>
<div class="">I quickly tested the latter process on CentOS6/MATLAB R2013b to point at local JDK8 and was able to successfully load the Bio-Formats 6 toolbox.</div>
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<span class=""></span><span class="">
<div class="">Can you try one of these options and let us know if you encounter more issues?</div>
</span><span class="">
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</span><span class="">
<div class="">From our side, we will clarify the impact of the Java bump for the MATLAB community in our technical documentation in an upcoming patch release. Thanks for bringing this problem to our attention.</div>
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<div class="">Best,</div>
<div class="">Sebastien</div>
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<div class="">[1] <a href="https://docs.openmicroscopy.org/bio-formats/6.0.0/about/whats-new.html" class="">https://docs.openmicroscopy.org/bio-formats/6.0.0/about/whats-new.html</a></div>
<div class="">[2] <a href="https://mathworks.com/help/matlab/release-notes.html?rntext=Java&startrelease=R2017b&endrelease=R2017b&category=advanced-software-development&groupby=release&sortby=descending&searchHighlight=Java" class="">https://mathworks.com/help/matlab/release-notes.html?rntext=Java&startrelease=R2017b&endrelease=R2017b&category=advanced-software-development&groupby=release&sortby=descending&searchHighlight=Java</a></div>
<div class="">[3] <a href="https://uk.mathworks.com/matlabcentral/answers/103056-how-do-i-change-the-java-virtual-machine-jvm-that-matlab-is-using-on-macos" class="">https://uk.mathworks.com/matlabcentral/answers/103056-how-do-i-change-the-java-virtual-machine-jvm-that-matlab-is-using-on-macos</a></div>
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<div class="">On 21 Feb 2019, at 12:06, Biofysikos Biologos <<a href="mailto:biofysikos@gmail.com" class="">biofysikos@gmail.com</a>> wrote:</div>
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<div class="">Hi David,<br class="">
<br class="">
Here are the results I get:<br class="">
<blockquote type="cite" class="">
<blockquote type="cite" class="">[status, version] = bfCheckJavaPath(true)<br class="">
</blockquote>
</blockquote>
<br class="">
status =<br class="">
<br class="">
logical<br class="">
<br class="">
0<br class="">
<br class="">
<br class="">
version =<br class="">
<br class="">
0×0 empty char array<br class="">
<br class="">
and yes the .jar file is in the same folder as the rest of the MATLAB scripts.<br class="">
<br class="">
Is it possible that my java version is not up to date? I am using R2017a.<br class="">
<br class="">
<blockquote type="cite" class="">
<blockquote type="cite" class="">version -java<br class="">
</blockquote>
</blockquote>
<br class="">
ans =<br class="">
<br class="">
'Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot(TM) 64-Bit<br class="">
Server VM mixed mode'<br class="">
<br class="">
Best,<br class="">
Biofysikos<br class="">
<br class="">
On Wed, Feb 20, 2019 at 3:04 PM David Gault (Staff)<br class="">
<<a href="mailto:d.gault@dundee.ac.uk" class="">d.gault@dundee.ac.uk</a>> wrote:<br class="">
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Hi Biofysikos,<br class="">
<br class="">
It looks as though the bioformats_package jar is not part of the MATLAB path.<br class="">
If you run the below it will quickly tell you if the jar can be found and if so which version.<br class="">
<br class="">
[status, version] = bfCheckJavaPath(true)<br class="">
<br class="">
Is the bioformats_package jar in the same folder as the rest of the MATLAB scripts?<br class="">
<br class="">
With Thanks,<br class="">
David Gault<br class="">
<br class="">
On 19 Feb 2019, at 20:48, Biofysikos Biologos <<a href="mailto:biofysikos@gmail.com" class="">biofysikos@gmail.com</a>> wrote:<br class="">
<br class="">
Hello,<br class="">
<br class="">
I have downloaded the latest Bioformats for MATLAB and it seems that<br class="">
the .jar file is not loading.<br class="">
<br class="">
The error I get is the following:<br class="">
<br class="">
Error using bfopen (line 100)<br class="">
Missing Bio-Formats library. Either add bioformats_package.jar to the<br class="">
static Java path or add it to the Matlab path.<br class="">
<br class="">
I have traced it to this line:<br class="">
<br class="">
reader = javaObject('loci.formats.in.FakeReader');<br class="">
<br class="">
Any help would be appreciated. Thanks.<br class="">
<br class="">
Biofysikos<br class="">
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