<div dir="ltr"><div>Hi Romain,<br><br></div>The <a href="http://loci.formats.BF">loci.formats.BF</a> class is part of bio-formats_plugins:<br><div><br>  $ jar tf $FIJI_HOME/plugins/bio-formats_plugins-5.8.2.jar|grep BF<br>  loci/plugins/BF.class<br>  loci/plugins/util/BFVirtualStack.class<br><br><div>Do not use bioformats_package.jar with Fiji; doing so will create problems with your classpath. See <a href="https://imagej.net/Uber-JAR">https://imagej.net/Uber-JAR</a>.<br></div><div><br></div><div>How is your IntelliJ project set up? Are you using Maven or Gradle? If so, which dependencies do you have declared? Have you read this guide: <a href="https://imagej.net/IDEA">https://imagej.net/IDEA</a> ?<br></div><div><br></div><div></div></div>Regards,<br><div>Curtis<br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><span style="font-size:12.8px">--</span></div><div><span style="font-size:12.8px">Curtis Rueden</span><br></div><div><span style="font-size:12.8px">LOCI software architect - <a href="https://loci.wisc.edu/software" target="_blank">https://loci.wisc.edu/software</a></span></div><div>ImageJ2 lead, Fiji maintainer - <span style="font-size:12.8px"><a href="https://imagej.net/User:Rueden" target="_blank">https://imagej.net/User:Rueden</a></span></div><div>Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" target="_blank">http://forum.imagej.net/</a></div><div><br></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, May 11, 2018 at 11:01 AM, Laine, Romain <span dir="ltr"><<a href="mailto:r.laine@ucl.ac.uk" target="_blank">r.laine@ucl.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">





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<p class="MsoNormal">Hi David,<u></u><u></u></p>
<p class="MsoNormal">Yes, using bioformats_package.jar file from the download link works fine !
<u></u><u></u></p>
<p class="MsoNormal">Many thanks. I am just not sure why the default bio-formats_plugins.jar in Fiji does not contain all the components.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thanks again !<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Romain<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">ome-devel <<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-devel-bounces@lists.<wbr>openmicroscopy.org.uk</a>> on behalf of "David Gault (Staff)" <<a href="mailto:d.gault@dundee.ac.uk" target="_blank">d.gault@dundee.ac.uk</a>><br>
<b>Reply-To: </b>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.<wbr>openmicroscopy.org.uk</a>><br>
<b>Date: </b>Friday, 11 May 2018 at 16:41<br>
<b>To: </b>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.<wbr>openmicroscopy.org.uk</a>><br>
<b>Subject: </b>Re: [ome-devel] Loci.formats missing<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><a name="m_7191149373661288148__MailOriginalBody">Hi Romain, <u></u><u></u></a></p>
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<p class="MsoNormal"><span><u></u> <u></u></span></p>
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<p class="MsoNormal"><span>The simplest approach is likely to use the Bio-Formats package from </span><a href="https://www.openmicroscopy.org/bio-formats/downloads/" target="_blank"><span>https://www.<wbr>openmicroscopy.org/bio-<wbr>formats/downloads/</span><span></span></a><span> which
 contains all of the components and necessary dependencies to read images in ImageJ.<u></u><u></u></span></p>
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<p class="MsoNormal"><span><u></u> <u></u></span></p>
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<p class="MsoNormal"><span>Alternatively below you can find a list of the individual components (you will likely need the listed core components) along with a Maven example of how to add the components to your project:<u></u><u></u></span></p>
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<p class="MsoNormal"><span></span><a href="https://docs.openmicroscopy.org/bio-formats/5.8.2/developers/components.html" target="_blank"><span>https://docs.openmicroscopy.<wbr>org/bio-formats/5.8.2/<wbr>developers/components.html</span><span></span></a><span><u></u><u></u></span></p>
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<p class="MsoNormal"><span></span><a href="https://github.com/ome/bio-formats-examples/blob/master/pom.xml" target="_blank"><span>https://github.com/ome/bio-<wbr>formats-examples/blob/master/<wbr>pom.xml</span><span></span></a><span><u></u><u></u></span></p>
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<p class="MsoNormal"><span><u></u> <u></u></span></p>
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<p class="MsoNormal"><span>With thanks,<u></u><u></u></span></p>
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<p class="MsoNormal"><span>David Gault<u></u><u></u></span></p>
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<p class="MsoNormal"><span><u></u> <u></u></span></p>
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<p class="MsoNormal"><span>On 11 May 2018, at 15:58, Laine, Romain <</span><a href="mailto:r.laine@ucl.ac.uk" target="_blank"><span>r.laine@ucl.ac.uk</span><span></span></a><span>>
 wrote:<u></u><u></u></span></p>
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<p class="MsoNormal"><span><u></u> <u></u></span></p>
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<p class="MsoNormal"><span>Dear list,</span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span>I am developing an ImageJ java plugin using bio-format to load .sdt files using IntelliJ IDEA.</span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span>I am trying to use the openImagePlus method as described in the Simple_Read.java example.</span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span>However the loci.formats package seems to be missing from the bio-formats_plugins and therefore cannot be imported, so I cannot handle exceptions from openImagePlus.</span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span>I am using the latest build bio-formats_plugins-5.9.0-<wbr>20180430.142015-2.jar</span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span> </span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span>Has anyone encountered/solved that problem?</span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span> </span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span>Many thanks !</span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span> </span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span>Romain</span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span> </span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span> </span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span><span style="font-size:10.0pt">______________________________<wbr>______</span></span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span><b><span style="font-size:10.0pt">Dr Romain F. Laine</span></b></span><span><span style="font-size:10.0pt">, PhD in Biophotonics</span></span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span><span style="font-size:10.0pt">PDRA at the Quantitative Imaging and Nanobiophysics group</span></span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span><span style="font-size:10.0pt">MRC Laboratory of Molecular Cell Biology (LMCB)</span></span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span><span style="font-size:10.0pt">University College London</span></span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span><span style="font-size:10.0pt">Gower Street, London, WC1E 6BT</span></span><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span></span><a href="http://www.ucl.ac.uk/lmcb/users/romain-laine" target="_blank"><span><span style="font-size:10.0pt;color:#0563c1">http://www.ucl.ac.uk/lmcb/<wbr>users/romain-laine</span></span><span></span></a><span><span style="font-size:12.0pt"><u></u><u></u></span></span></p>
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<p class="MsoNormal"><span><span style="font-size:12.0pt"> <u></u><u></u></span></span></p>
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<p class="MsoNormal"><span><u></u> <u></u></span></p>
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<p class="MsoNormal"><span><br>
</span><span><span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span></span><span>
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