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Matlab and the Micro-Manager GUI

You can use Matlab to run and control the Micro-Manager gui and core. Here's how (examples shown using version 1.4.11; use the most recent version you have installed):

1. In Matlab, type

>> edit classpath.txt

and add the following lines, adjusting the path if necessary:

C:/Program Files/Micro-Manager-1.4.11/ij.jar
C:/Program Files/Micro-Manager-1.4.11/plugins/Micro-Manager/MMCoreJ.jar
C:/Program Files/Micro-Manager-1.4.11/plugins/Micro-Manager/MMJ_.jar
C:/Program Files/Micro-Manager-1.4.11/plugins/Micro-Manager/bsh-2.0b4.jar
C:/Program Files/Micro-Manager-1.4.11/plugins/Micro-Manager/swingx-0.9.5.jar
C:/Program Files/Micro-Manager-1.4.11/plugins/Micro-Manager/swing-layout-1.0.4.jar

you will need the additional items below in the classpath.txt to use the multi-image file format:

C:/Program Files/Micro-Manager-1.4.11/plugins/Micro-Manager/ome-xml.jar
C:/Program Files/Micro-Manager-1.4.11/plugins/Micro-Manager/loci-common.jar
C:/Program Files/Micro-Manager-1.4.11/plugins/Micro-Manager/scifio.jar
C:/Program Files/Micro-Manager-1.4.11/plugins/Micro-Manager/slf4j-api-1.7.1.jar

2. Again in Matlab, type

>> edit librarypath.txt

and add the line:

C:/Program Files/Micro-Manager-1.4

3. Restart Matlab. Now type the following at the command prompt:

>> cd 'c:/program files/Micro-Manager-1.4'
>> import org.micromanager.MMStudio;
>> gui = MMStudio(false);
>> mmc = gui.getCore;
>> acq = gui.getAcquisitionEngine;

Now you have gui, mmc, and acq objects that you can control from Matlab, very similar to how you would in Beanshell scripts.

On Mac OS X, current versions of Matlab have a bug that causes Micro-Manager to fail on startup. To work around this bug, issue the following command before starting the Micro-Manager GUI:

>> java.lang.System.clearProperty('java.util.prefs.PreferencesFactory')

(Reported by Paul Andrews, work around suggested by The Mathworks support).

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