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<p class="MsoNormal">Hi David,<o:p></o:p></p>
<p class="MsoNormal">Yes, using bioformats_package.jar file from the download link works fine !
<o:p></o:p></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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks again !<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Romain<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></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 <ome-devel-bounces@lists.openmicroscopy.org.uk> on behalf of "David Gault (Staff)" <d.gault@dundee.ac.uk><br>
<b>Reply-To: </b>OME External Developer List <ome-devel@lists.openmicroscopy.org.uk><br>
<b>Date: </b>Friday, 11 May 2018 at 16:41<br>
<b>To: </b>OME External Developer List <ome-devel@lists.openmicroscopy.org.uk><br>
<b>Subject: </b>Re: [ome-devel] Loci.formats missing<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a name="_MailOriginalBody">Hi Romain, <o:p></o:p></a></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">The simplest approach is likely to use the Bio-Formats package from </span><a href="https://www.openmicroscopy.org/bio-formats/downloads/"><span style="mso-bookmark:_MailOriginalBody">https://www.openmicroscopy.org/bio-formats/downloads/</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"> which
contains all of the components and necessary dependencies to read images in ImageJ.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"></span><a href="https://docs.openmicroscopy.org/bio-formats/5.8.2/developers/components.html"><span style="mso-bookmark:_MailOriginalBody">https://docs.openmicroscopy.org/bio-formats/5.8.2/developers/components.html</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"></span><a href="https://github.com/ome/bio-formats-examples/blob/master/pom.xml"><span style="mso-bookmark:_MailOriginalBody">https://github.com/ome/bio-formats-examples/blob/master/pom.xml</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">With thanks,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">David Gault<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">On 11 May 2018, at 15:58, Laine, Romain <</span><a href="mailto:r.laine@ucl.ac.uk"><span style="mso-bookmark:_MailOriginalBody">r.laine@ucl.ac.uk</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody">>
wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Dear list,</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">I am developing an ImageJ java plugin using bio-format to load .sdt files using IntelliJ IDEA.</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">I am trying to use the openImagePlus method as described in the Simple_Read.java example.</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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 style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">I am using the latest build bio-formats_plugins-5.9.0-20180430.142015-2.jar</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> </span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Has anyone encountered/solved that problem?</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> </span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Many thanks !</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> </span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Romain</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> </span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> </span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt">____________________________________</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><b><span style="font-size:10.0pt">Dr Romain F. Laine</span></b></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt">, PhD in Biophotonics</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt">PDRA at the Quantitative Imaging and Nanobiophysics group</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt">MRC Laboratory of Molecular Cell Biology (LMCB)</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt">University College London</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt">Gower Street, London, WC1E 6BT</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"></span><a href="http://www.ucl.ac.uk/lmcb/users/romain-laine" target="_blank"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;color:#0563C1">http://www.ucl.ac.uk/lmcb/users/romain-laine</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt;font-family:Helvetica">_______________________________________________<br>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><br>
</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span></span><span style="mso-bookmark:_MailOriginalBody">
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