Linux installation from source (Ubuntu)
Contents
Preparation
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
Other Required 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
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 https://valelab.ucsf.edu/svn/micromanager2/trunk/ micro-manager1.4 svn co https://valelab.ucsf.edu/svn/3rdpartypublic/
This creates 2 new folders in the mm
directory:
~/mm/micro-manager1.4 ~/mm/3rdpartypublic
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 ./mmUnixBuild.sh ./configure --with-imagej=/usr/local/ImageJ
Compile
make
Install
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
.
#!/bin/bash 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 \ ij.ImageJ
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
Appendix
Dependencies
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) |