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

(Install: New install-ijplugin target; no need for ldconfig as Micro-Manager does not install any shared libraries that are not dlopened.)
(Create the startup script: Launch script is now created by make.)
Line 83: Line 83:
= Post Install =
= Post Install =
== Create the startup script ==
== Editing the startup script ==
Micro-Manager requires the path to <code>/usr/local/lib/micro-manager</code>. Create the 4 line Bash script below in <code>/usr/local/ImageJ</code> and save it as, say, <code>/usr/local/bin/mmscript</code>.
A script named <code>mmimagej</code> will have been installed in <code>/usr/local/ImageJ</code>. You might want to edit its contents to pass extra flags to Java. You may also want to put this script in your <code>PATH</code>.
{{MessageBox|1=File: mmscript|2=<pre>
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 =
= Running Micro-Manager =

Revision as of 16:35, 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

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 autoconf 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:


Building Micro-Manager

Create the Autotools files


cd ~/mm/micro-manager1.4
./configure --enable-imagej-plugin=/usr/local/ImageJ






sudo make install-ijplugin
If you have run ./configure without --enable-imagej-plugin, you will be running sudo make install instead. See the build documentation for details.

Post Install

Editing the startup script

A script named mmimagej will have been installed in /usr/local/ImageJ. You might want to edit its contents to pass extra flags to Java. You may also want to put this script in your PATH.

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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