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

[Tim C]

OK,
that was stupid :)

It worked much better when I placed the loci_tools.jar in the image
folder and passed the full path to bfopen. So
> data=bfopen('20090423 field 1-2009-0002.zvi');
 should have been (e.g.)
> data=bfopen('C:\20090423 field 1-2009-0002.zvi');
Hopefully this mail can help the next guy :)

//Tim


Tim C wrote:
> Hello list, this is my first post. I hope this is the right place to ask.
>
> I want to open Zeiss ZVI microscope images in Matlab, and did as
> described on http://www.loci.wisc.edu/ome/formats-matlab.html
> meaning I downloaded bfopen.m and placed loci_tools.jar in my c:\Matlab\work
>
> data=bfopen('20090423 field 1-2009-0002.zvi'); %where the zvi is an
> existing file
>
> results in
>   
>> ??? Undefined variable "loci" or class "loci.formats.ChannelFiller".
>>
>> Error in ==> bfopen at 40
>> r = loci.formats.ChannelFiller();
>>     
> c:\matlab\work is in my path.
>
> I am using Matlab 7.0.1.24704 (R14) Service Pack 1 on Windows XP pro
> SP3. I downloaded
> loci_tools.jar    4.0.0 (stable release)      2009 Mar 3
>   
>> version -java is "Java 1.4.2_04 with Sun Microsystems Inc. Java
>> HotSpot(TM) Client VM (mixed mode)"
>>     
>
> My question: Do I need to do something to the bfopen.m script to adapt
> it to my installation (I'm not aware that it's in any way
> unusual/special)? Why doesn't "loci" seem to be defined? What am I doing
> wrong?
>
>
> All help is greatly appreciated!
>
> //Tim
>
>