[ImageJ-devel] Question about Bioformats, Scifio and ImageJ 2.0

[Curtis Rueden]

Hi Birgit,


> loci-common-4.4-imagej-2.0.0-beta2.1.jar
> ome-xml-4.4-imagej-2.0.0-beta2.1.jar
> poi-loci-4.4-imagej-2.0.0-beta2.1.jar
> scifio-4.4-imagej-2.0.0-beta2.1.jar


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



They all seem to contain parts of the Bioformats/Loci/OME-XML libraries.
> It appears that most of the contents of these libraries have formerly
> been part of loci_tools.jar. Our question is in how far these libraries
> are compatible (or even equal?) to the other (older?) ones which can be
> downloaded from the Bioformats page, i.e. loci_tools.jar.


The loci_tools.jar is a convenience bundle of bio-formats.jar plus its
dependencies. For details, see:
    http://loci.wisc.edu/bio-formats/bio-formats-java-library#jars

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).


> The thing is that our software is supposed to principally run in ImageJ
> 1.0 as well as in 2.0. Therefore it would be great if we could rely on
> just one version of bioformats, i.e. either loci_tools or the four
> libraries from above.


You should be able to rely on a single version of Bio-Formats without
problems (ideally the latest version).

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.

Regards,
Curtis


On Thu, Jul 5, 2012 at 9:40 AM, Birgit Moeller <
birgit.moeller at informatik.uni-halle.de> wrote:

> Dear ImageJ 2.0 team!
> We try to some prototypical development of some plugins (and something
> more) on top of the ImageJ 2.0 core. ImageJ 2.0 comes with lots of jars.
> Among them there are the following four
>
> loci-common-4.4-imagej-2.0.0-beta2.1.jar
> ome-xml-4.4-imagej-2.0.0-beta2.1.jar
> poi-loci-4.4-imagej-2.0.0-beta2.1.jar
> scifio-4.4-imagej-2.0.0-beta2.1.jar
>
> They all seem to contain parts of the Bioformats/Loci/OME-XML libraries.
> It appears that most of the contents of these libraries have formerly
> been part of loci_tools.jar. Our question is in how far these libraries
> are compatible (or even equal?) to the other (older?) ones which can be
> downloaded from the Bioformats page, i.e. loci_tools.jar.
>
> The thing is that our software is supposed to principally run in ImageJ
> 1.0 as well as in 2.0. Therefore it would be great if we could rely on
> just one version of bioformats, i.e. either loci_tools or the four
> libraries from above. Could you give us a hint which option to follow,
> i.e. which libraries to use, or should it even be possible to use both
> in common?
> Is the version shipped with ImageJ 2.0 just a new release of
> Bioformats/Loci not yet available on the webpage (...but which will be
> available there in near future)?
> Or does that version contain ImageJ 2.0 specific changes which make
> sense only in the context of ImageJ 2.0, and Bioformats/Loci as
> available for ImageJ 1.0 from the webpage will become/remain something
> different?
>
> It would be great if you could clarify this a bit.
> Thanks a lot and best regards,
>
>  Birgit
>
> ------------------------------------------------------------------------
> Dr. rer. nat. Birgit Moeller  Pattern Recognition & Bioinformatics
>                               Institute of Computer Science
>  phone:   +49(0)345-55-24745  Faculty of Natural Sciences III
>  fax:     +49(0)345-55-27039  Martin Luther University Halle-Wittenberg
>  office:  Room 4.12           Von-Seckendorff-Platz 1
>                               06099 Halle / Saale (Germany)
>
> e-mail:  birgit.moeller at informatik.uni-halle.de
> www:     http://www.informatik.uni-halle.de/moeller/
> ------------------------------------------------------------------------
>
>
>
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