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Difference between revisions of "Linux installation from source (Ubuntu)"

(Install JDK: OpenJDK is recommended.)
(OpenJDK is default method.)
Line 167: Line 167:
| Andor SDK 2/3 || N/A - request from Andor website
| Andor SDK 2/3 || N/A - request from Andor website
== OpenJDK instead of Sun JDK ==
It may be possible to also use the distro-friendly OpenJDK (<code>default-jdk</code>) without too much effort. To start, you would have to patch the Micro-Manager <code></code> file to find <code>jni.h</code>[] and possibly apply other fixes.

Revision as of 17:28, 22 April 2014


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

Ensure you don't have the Ubuntu package installed:


sudo apt-get purge 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 micro-manager1.4
svn co

This creates 2 new folders in the mm directory:


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
./configure --with-imagej=/usr/local/ImageJ \






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.

File: mmscript

cd /usr/local/ImageJ
java -Xmx1439m -Xincgc -XX:PermSize=128m \
     -Dpython.cachedir.skip=true -Dplugins.dir=/usr/local/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 &



You need the following packages:
Name Equivalent Synaptic package name
Required Dependencies:
Subversion subversion
GNU C++ build-essential
GNU Autotools automake
GNU Libtool libtool
Boost libraries libboost-all-dev
zlib compression library zlib1g-dev
Simplified Wrapper and Interface Library swig
Sun Java SDK N/A - manually fetch from Oracle website
Optional Dependencies:
Firewire Camera Library libdc1394-*-dev
Open Source Computer Vision Library libopencv-dev
Andor SDK 2/3 N/A - request from Andor website
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