Preparation

Install JDK

If you are building the Micro-Manager Java GUI, Java 1.6 or 1.7 is recommended[1]. The simplest way is to use OpenJDK:

sudo apt-get install openjdk-6-jdk

(You can also use openjdk-7-jdk.)

Install ImageJ

Download the Linux version of ImageJ from the NIH website. From a terminal, unzip to /usr/local/, and remove the embedded JRE, as we already have one installed.

cd ~/Downloads/
sudo unzip ij*-linux*.zip -d /usr/local/
sudo rm -rf /usr/local/ImageJ/jre
sudo chmod a+Xr /usr/local/ImageJ

Install Build Programs and Libraries

You will need a subversion client to checkout the source code, several libraries, and build tools. Install them with:

sudo apt-get install subversion build-essential automake libtool \
                     libboost-all-dev zlib1g-dev swig

You may also need to install additional packages (for cameras and special hardware). See the full list in #Dependencies

Fetch Source Repositories

Create a directory for the the subversion repositories, such as ~/mm. Besides the source tree, additional binary dependencies are stored in the 3rdpartypublic repository. The build scripts in the source tree assume 3rdpartypublic is in the same parent folder level:

mkdir ~/mm
cd ~/mm
svn co https://valelab.ucsf.edu/svn/micromanager2/trunk/ micro-manager1.4
svn co https://valelab.ucsf.edu/svn/3rdpartypublic/

This creates 2 new folders in the mm directory:

    ~/mm/micro-manager1.4
    ~/mm/3rdpartypublic

Add the Beanshell and SwingX to the ImageJ plugins directory:

cd ~/mm/3rdpartypublic/classext
sudo cp bsh-2.0b4.jar swingx-0.9.5.jar /usr/local/ImageJ/plugins/

Building Micro-Manager

Create the Autotools files

configure uses the bundled version of ImageJ:

cd ~/mm/micro-manager1.4
./mmUnixBuild.sh
./configure --with-imagej=/usr/local/ImageJ \
            --with-javaincl=/usr/lib/jvm/java-7-oracle/include/

Compile

make

Install

sudo make install
sudo ldconfig

Post Install

Create the startup script

Micro-Manager requires the path to /usr/local/lib/micro-manager. Create the 4 line Bash script below in /usr/local/ImageJ and save it as, say, /usr/local/bin/mmscript.

#!/bin/bash
cd /usr/local/ImageJ
java -Xmx1439m -Xincgc -XX:PermSize=128m \
     -Dpython.cachedir.skip=true -Dplugins.dir=/usr/local/ImageJ \
     -Dsun.java.command=ImageJ -Djava.class.path=/usr/local/ImageJ/ij.jar \
     -Dimagej.dir=/usr/local/ImageJ -Dij.dir=/usr/local/ImageJ \
     -Dij.executable=/usr/local/ImageJ/ImageJ \
     -Djava.library.path=/usr/share/java:/usr/local/lib/micro-manager \
      ij.ImageJ -eval 'run("Micro-Manager Studio");'

Make the script executable:

sudo chmod +x mmscript

Running Micro-Manager

Start Micro-Manager with your new script:

./mmscript &

Appendix

Dependencies