[ome-users] Newbee question bio-formats in Matlab

[Melissa Linkert]

Hi Claudia,

The installation steps that you describe are correct - just to be
sure, I tried them on a fresh install of  Matlab 7.0.4, and was able
to run the bfopen command without any problems.

There are a few possible reasons for seeing this error message:

 - Matlab was not restarted after 'classpath.txt' was edited
 - changes 'classpath.txt' somehow did not get saved
 - the JVM being used by Matlab is version 1.4 or earlier

To check the last possibility, run the "version -java" command;
Bio-Formats requires Java 1.5 or later, so you will need to upgrade if
the reported version number is 1.4 or lower.  Instructions for
upgrading Matlab's JVM are available here:

http://www.mathworks.com/access/helpdesk/help/techdoc/matlab_external/f98533.html#f122001

Please let us know if none of these suggestions solve the problem.

Regards,
-Melissa

On Tue, Jan 12, 2010 at 8:48 AM, Claudia Dach <cdach at gmx.de> wrote:
> Hi,
>
> there was already a topic of importing zvi-files to Matlab. I tried to do
> it, but it didn't work. I saved the "loci_tools.jar" to
> "C:\Programme\MATLAB_SV7\java\jar".
>
> In the "classpath.txt" which I found under the path
> "C:\Programme\MATLAB_SV7\toolbox\local", I just added the line
> "$matlabroot/java/jar/loci_tools.jar" (is this it what you meant with
> updating?).
>
> The "bfopen.m"-file I saved under "C:\Programme\MATLAB_SV7\work".
>
> When I then type in the command "data=bfopen('C:\Hela.zvi')", I always get
> back this error:
>
> ??? Undefined variable "loci" or class "loci.formats.ChannelFiller".
>
> Error in ==> bfopen at 43
> r = loci.formats.ChannelFiller();
>
> Could you tell me which step I'm doing wrong?
>
> Thanks a lot!
> claudia
>
>
> --
> Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox 3.5 -
> sicherer, schneller und einfacher! http://portal.gmx.net/de/go/chbrowser
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>