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Linux installation from source (Ubuntu)

Revision as of 15:37, 23 August 2013 by P.nanda (Talk | contribs)


Install ImageJ

Download the Linux version of ImageJ from the NIH website. From a terminal, unzip to /usr/local/ and test that it runs:


cd ~/Downloads/
sudo unzip ij*-linux*.zip -d /usr/local/
sudo chmod +r /usr/local/ImageJ
cd /usr/local/ImageJ/
./jre/bin/java -jar ij.jar

Install JDK

If you are building the Micro-Manager Java GUI, Java 1.6 is recommended[1]. This has to be fetched from Oracle's website since their licensing prohibits redistribution in Linux repositories. Download the latest jdk-6*-linux-*.bin from the archives (you must click "Accept License Agreement").

It may be possible to also use the distro-friendly OpenJDK (default-jdk) without too much effort. To start, you would have to patch the Micro-Manager configure file to find jni.h and possibly apply other fixes.

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/

Create a new micro-manager directory in /usr/lib/


sudo mkdir /usr/lib/micro-manager

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

File: mmscript

cd /usr/local/ImageJ
export LD_LIBRARY_PATH=.:/usr/local/lib:/usr/lib/micro-manager:/usr/local/ImageJ
java -mx1200m \
     -Djava.library.path=/usr/lib/micro-manager:/usr/local/ImageJ \
     -Dplugins.dir=/usr/local/ImageJ \
     -cp /usr/local/ImageJ/ij.jar:usr/local/jdk1.5.0_04/lib/tools.jar \

Make the script executable:


sudo chmod +x mmscript

Running Micro-Manager

Start ImageJ with your new script:


./mmscript &

Run Plugins > Micro-Manager > Micro-Manager Studio



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 openjdk-6-jdk
Optional Dependencies:
Firewire Camera Library libdc1394-*-dev
Open Source Computer Vision Library libopencv-dev
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