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

[dzmacdonald]

Hi Tim,

Another solution to this would be to add the jar to the MatlabDir/java/ 
libs directory
and then update the classpath.txt in MatlabDir/local/toolbox/ 
classpath.txt

you may also be interested in, which also has a description of using  
java in matlab.

http://trac.openmicroscopy.org.uk/omero/wiki/OmeroMatlab

Regards

D.


On Apr 27, 2009, at 1:31 PM, Tim C wrote:

> 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
>>
>>
>
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