Hi Birgit,<div><br></div><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><br>loci-common-4.4-imagej-2.0.0-beta2.1.jar<br>
ome-xml-4.4-imagej-2.0.0-beta2.1.jar<br>poi-loci-4.4-imagej-2.0.0-beta2.1.jar<br>scifio-4.4-imagej-2.0.0-beta2.1.jar</blockquote><div><br></div><div>The "4.4-imagej-2.0.0-beta2.1" release is a version that we built for ImageJ2, off the latest develop branch of bioformats.git. There are no special hacks or changes specific to ImageJ2; we simply needed the latest bugfixes and API changes in order for ImageJ2's file I/O to work properly. We are hoping to avoid this sort of custom-built version in the future, after the OME 4.4 release, when we expect to have </div>
<div><br></div><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"> </blockquote><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
They all seem to contain parts of the Bioformats/Loci/OME-XML libraries.<br>It appears that most of the contents of these libraries have formerly<br>been part of loci_tools.jar. Our question is in how far these libraries<br>
are compatible (or even equal?) to the other (older?) ones which can be<br>downloaded from the Bioformats page, i.e. loci_tools.jar.</blockquote><div><br></div><div>The loci_tools.jar is a convenience bundle of bio-formats.jar plus its dependencies. For details, see:</div>
<div> <a href="http://loci.wisc.edu/bio-formats/bio-formats-java-library#jars">http://loci.wisc.edu/bio-formats/bio-formats-java-library#jars</a></div></div></div><div><br></div><div>Regarding compatibility, you should be free to mix and match your own version of the Bio-Formats code, particularly newer versions (since we try not to break backwards compatibility).</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><br>The thing is that our software is supposed to principally run in ImageJ<br>
1.0 as well as in 2.0. Therefore it would be great if we could rely on<br>just one version of bioformats, i.e. either loci_tools or the four<br>libraries from above.</blockquote><div><br></div><div>You should be able to rely on a single version of Bio-Formats without problems (ideally the latest version).</div>
<div><br></div><div>The question of whether to use loci_tools.jar or bio-formats.jar + dependencies is up to you; every developer likes to do things his/her own way. That said, if you want my personal advice, I would suggest structuring your code as a Maven project, which makes dependency management much easier and gives your project a standardized build process. Then you don't have to worry about juggling JARs yourself nearly so much. I would be happy to elaborate further and/or provide code examples if you are interested; just let me know.</div>
<div><br></div><div>Regards,</div><div>Curtis</div><div><br></div><br><div class="gmail_quote">On Thu, Jul 5, 2012 at 9:40 AM, Birgit Moeller <span dir="ltr"><<a href="mailto:birgit.moeller@informatik.uni-halle.de" target="_blank">birgit.moeller@informatik.uni-halle.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear ImageJ 2.0 team!<br>
We try to some prototypical development of some plugins (and something<br>
more) on top of the ImageJ 2.0 core. ImageJ 2.0 comes with lots of jars.<br>
Among them there are the following four<br>
<br>
loci-common-4.4-imagej-2.0.0-beta2.1.jar<br>
ome-xml-4.4-imagej-2.0.0-beta2.1.jar<br>
poi-loci-4.4-imagej-2.0.0-beta2.1.jar<br>
scifio-4.4-imagej-2.0.0-beta2.1.jar<br>
<br>
They all seem to contain parts of the Bioformats/Loci/OME-XML libraries.<br>
It appears that most of the contents of these libraries have formerly<br>
been part of loci_tools.jar. Our question is in how far these libraries<br>
are compatible (or even equal?) to the other (older?) ones which can be<br>
downloaded from the Bioformats page, i.e. loci_tools.jar.<br>
<br>
The thing is that our software is supposed to principally run in ImageJ<br>
1.0 as well as in 2.0. Therefore it would be great if we could rely on<br>
just one version of bioformats, i.e. either loci_tools or the four<br>
libraries from above. Could you give us a hint which option to follow,<br>
i.e. which libraries to use, or should it even be possible to use both<br>
in common?<br>
Is the version shipped with ImageJ 2.0 just a new release of<br>
Bioformats/Loci not yet available on the webpage (...but which will be<br>
available there in near future)?<br>
Or does that version contain ImageJ 2.0 specific changes which make<br>
sense only in the context of ImageJ 2.0, and Bioformats/Loci as<br>
available for ImageJ 1.0 from the webpage will become/remain something<br>
different?<br>
<br>
It would be great if you could clarify this a bit.<br>
Thanks a lot and best regards,<br>
<br>
Birgit<br>
<br>
------------------------------------------------------------------------<br>
Dr. rer. nat. Birgit Moeller Pattern Recognition & Bioinformatics<br>
Institute of Computer Science<br>
phone: +49(0)345-55-24745 Faculty of Natural Sciences III<br>
fax: +49(0)345-55-27039 Martin Luther University Halle-Wittenberg<br>
office: Room 4.12 Von-Seckendorff-Platz 1<br>
06099 Halle / Saale (Germany)<br>
<br>
e-mail: <a href="mailto:birgit.moeller@informatik.uni-halle.de">birgit.moeller@informatik.uni-halle.de</a><br>
www: <a href="http://www.informatik.uni-halle.de/moeller/" target="_blank">http://www.informatik.uni-halle.de/moeller/</a><br>
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<br></blockquote></div><br></div>