[ome-devel] loci-plugins vs bio-formats

[Grabmayr, Heinrich]

Hi there,

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.

up to now, I had used loci-plugins4.4 as a dependency
                               <dependency>
                                               <groupId>loci</groupId>
                                               <artifactId>loci_plugins</artifactId>
                                               <version>4.4-SNAPSHOT</version>
                               </dependency>

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Bioformats gone!"), Fiji reported issues about duplicate commands which led me to believe that loci_plugins.jar has been replaced by bio-formats.jar (the imagej-maven index [1] tells me that there is such a jar), so I replaced the dependency to
                               <dependency>
                                               <groupId>loci</groupId>
                                               <artifactId>bio-formats</artifactId>
                                               <version>5.0-SNAPSHOT</version>
                               </dependency>

but compiling fails because then, the package loci.plugins does not exist.

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.

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 http://maven.imagej.net/content/groups/public" (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??

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..

Thanks
    Heinrich

[1] http://maven.imagej.net:8081/index.html#nexus-search;quick~bio-formats
[2] http://downloads.openmicroscopy.org/bio-formats/5.0.0/#api


Heinrich Grabmayr

Technische Universität München
E27 cellular biophysics
James-Franck-Str.1
85748 Garching
Tel: +49 89 289 12487

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