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<p class="MsoNormal">Hi there,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US">I have written a few ImageJ plugins that use bio-formats. They used to work until I got confused with the introduction of bio-formats 5.0, so I would be grateful for help on that.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">up to now, I had used loci-plugins4.4 as a dependency<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <dependency><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <groupId>loci</groupId><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <artifactId>loci_plugins</artifactId><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <version>4.4-SNAPSHOT</version><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> </dependency><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">after updating Fiji to include new bio-formats jars (as suggested by Curtis in “Re: [ome-users] Bioformats gone!”), Fiji reported issues about duplicate commands which led me to believe that loci_plugins.jar has been
replaced by bio-formats.jar (the imagej-maven index [1] tells me that there is such a jar), so I replaced the dependency to<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <dependency><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <groupId>loci</groupId><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <artifactId>bio-formats</artifactId><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <version>5.0-SNAPSHOT</version><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> </dependency><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">but compiling fails because then, the package loci.plugins does not exist.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I checked on the bio-formats download website [2], and found various jars, but neither loci_plugins, nor bio-formats. The bio-formats API tells me that the loci.plugins.util.LibraryChecker exists, but not in which jar
it is.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Then I figured that maybe a few classes may have been transferred from loci_plugins to bio-formats, so the issue may be resolved by using loci_plugins 5.0. With this dependency, however, my plugin does not compile, telling
me “Failure to find imagej:ij:jar:1.43u in <a href="http://maven.imagej.net/content/groups/public">
http://maven.imagej.net/content/groups/public</a>” (I am using the latest imagej version ${imagej1.version} as a dependency). This error reproducibly happens with loci_plugins 5.0 and not with 4.4. That totally confuses me because whether or not maven can find
an imagej version should not depend on the version of loci_plugins, should it??<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Can anyone help me with this specific issue? And more generally, I am afraid I missed a crucial starting point on how to know how to find stuff. Usually, I google for the API and then get clues by the package names..<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> Heinrich<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">[1] <a href="http://maven.imagej.net:8081/index.html#nexus-search;quick~bio-formats">
http://maven.imagej.net:8081/index.html#nexus-search;quick~bio-formats</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">[2] <a href="http://downloads.openmicroscopy.org/bio-formats/5.0.0/#api">
http://downloads.openmicroscopy.org/bio-formats/5.0.0/#api</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;mso-fareast-language:DE">Heinrich Grabmayr<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;mso-fareast-language:DE">Technische Universität München<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;mso-fareast-language:DE">E27 cellular biophysics<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt;mso-fareast-language:DE">James-Franck-Str.1<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt;mso-fareast-language:DE">85748 Garching<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt;mso-fareast-language:DE">Tel: +49 89 289 12487</span><span lang="EN-US" style="mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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