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

(Readd ImageJ installation notes)
(Require /usr/local path since Micro-Manager build scripts expect it there.)
Line 3: Line 3:
=== Install ImageJ ===
=== Install ImageJ ===
[ Download the Linux version of ImageJ] from the NIH website and follow the installation instructions thereTest that ImageJ runs from a terminal:
[ Download the Linux version of ImageJ] from the NIH website.  From a terminal, unzip to <code>/usr/local/</code> and test that it runs:
cd ~/Downloads/
sudo unzip ij*-linux*.zip -d /usr/local/
cd /usr/local/ImageJ/
cd /usr/local/ImageJ/

Revision as of 13:18, 23 August 2013


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/
cd /usr/local/ImageJ/

Other Required Programs and Libraries

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

Heavy editing in progress: some dependencies may be missing

sudo apt-get install subversion build-essential automake libtool \
                     libboost-all-dev zlib1g-dev swig sun-java6-sdk

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

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 sun-java6-sdk
Optional Dependencies:
Firewire Camera Library libdc1394-*-dev
Open Source Computer Vision Library (FIXME)
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