Linux installation from source (Ubuntu)
Preparation
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 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
Building Micro-Manager
Create the Autotools files
cd ~/mm/micro-manager1.4 ./autogen.sh ./configure --enable-imagej-plugin=/usr/local/ImageJ
Compile
make
Install
sudo make install-ijplugin
./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 by typing:
/usr/local/ImageJ/mmimagej 2>&1 >/dev/null &
To view the Core logging in the terminal while Micro-Manager is running, start simply as:
/usr/local/ImageJ/mmimagej
Appendix
Dependencies
Name | Equivalent Synaptic package name |
---|---|
Required Dependencies: | |
Subversion | subversion
|
GNU C++ | build-essential
|
GNU Autotools | autoconf , automake
|
GNU Libtool | libtool
|
Boost libraries | libboost-all-dev
|
zlib compression library | zlib1g-dev
|
Simplified Wrapper and Interface Library | swig
|
OpenJDK | openjdk-6-jdk or openjdk-7-jdk
|
Optional Dependencies: | |
Python | python-dev , python-numpy-dev
|
Firewire Camera Library | libdc1394-*-dev
|
Open Source Computer Vision Library | libopencv-dev
|
GPhoto2 | libgphoto2-2-dev
|
FreeImagePlus (used by GPhoto device adapter) | libfreeimage-dev
|
libusb 0.1 | libusb-dev
|
Andor SDK 2/3 | N/A - request from Andor website |