Posted by
ctrueden on
URL: http://imagej.273.s1.nabble.com/Bio-Formats-release-2006-Sep-27-tp3701231p3701235.html
Hi David,
A couple of notes:
1) The correct place for all JARs to be is the ImageJ plugins folder.
You should have loci_plugins.jar, bio-formats.jar, ome-java.jar and
poi-loci.jar in there.
All old copies of the Bio-Formats JARs should be REMOVED from the
/System/Library/Java/Extensions and /Library/Java/Extensions folders.
Previously, the installation instructions indicated that the support
libraries should be placed there, but doing so is actually not
necessary. Actually, older JAR files in those folders will actually
cause problems, so they should be removed.
I sincerely apologize for the confusion with the Extensions folder; I
did not realize ImageJ was cool that it loaded support libraries from
the plugins folder -- but it does. So installation is as simple as
just dropping everything into plugins.
2) I did hear from one person who had trouble running Bio-Formats on
the Mac with Java 1.4. Upgrading to 1.5 fixed her problem. But since
you are already running Java 1.5, this issue is not relevant to you.
(I mention it here in case anyone else on the list has had trouble
with Bio-Formats on the Mac, as one more thing to try.)
-Curtis
On 9/27/06, David Knecht-charter <
[hidden email]> wrote:
> I have so far been unable to run Bioformats on my MacBook Pro (OSX
> 10.4.7) and am wondering if anyone else is having the same problem.
> After installation of the files, LOCI shows up in my plugins list,
> but when I choose Biofromats Importer, nothing happens. On other
> computers in my lab it works fine with the same ImageJ and OSX
> version (1.36b, Java 1.5). Dave
>
> Dr. David Knecht
> Department of Molecular and Cell Biology
> U-3125
> 91 N. Eagleville Rd.
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
> 860-486-4331 (fax)
>
>
> On Sep 27, 2006, at 1:02 PM, Curtis Rueden wrote:
>
> > Hi,
> >
> > Today LOCI has released a new version of Bio-Formats. Major changes
> > include:
> >
> > * PerkinElmer: support for PE UltraView
> > * Openlab LIFF: support for Openlab v5
> > * Leica LEI: bugfixes, and support for multiple series
> > * ZVI, OIB, IPW: more robust handling of these formats (eliminated
> > custom OLE parsing logic in favor of Apache POI)
> > * OIB: better metadata parsing (but maybe still not perfect?)
> > * LSM: fixed a bug preventing import of certain LSMs
> > * Metamorph STK: fixed a bug resulting in duplicate image planes
> > * User interface: use of system look & feel for file chooser dialog
> > when available
> > * Better notification when JAR libraries are missing
> >
> > You can download the release from the Bio-Formats web site:
> >
http://www.loci.wisc.edu/ome/formats.html> >
> > Please note that there is one new library required, poi-loci.jar, in
> > addition to the old dependencies. It goes in the ImageJ plugins folder
> > just like the others.
> >
> > To receive future release notifications, sign up for the LOCI software
> > mailing list by following the instructions on the LOCI software web
> > site:
> >
http://www.loci.wisc.edu/software/> >
> > And as always, please let me know if you have any issues or questions
> > about the software.
> >
> > Cheers,
> > Curtis
>