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

(Large cleanup: proper formatting, dependencies moved to appendix.)
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== Post Install
== Post Install ==
=== Create the startup script ===
=== Create the startup script ===

Revision as of 12:48, 23 August 2013


Required Programs and Libraries

Heavy editing in progress: ImageJ install notes to be readded

Install ImageJ

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 libraries (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=../3rdpartypublic/classext






sudo make install
sudo ldconfig

Post Install

Create the startup script

Starting ImageJ with the scripts provided in the ImageJ directory (run, script, see 1 above) will start ImageJ, but Micro-Manager, although now in the plugins directory, will not work properly because the path to /usr/lib/micro-manager is missing. Write your own script containing the 4 lines given below ("mmscript"), save and move it to /usr/local/ImageJ.

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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