top bar

How To Build Micro Manager From Source On Ubuntu 13.10

Revision as of 15:29, 15 November 2013 by Hadim (Talk | contribs)

Here is a small script I use to build MM on Linux to be able to test news and develop plugin and script with DemoAdaptaters. I can provide help to adapt build system to your Linux. Contact me on the MM mailing list:

Command Line

# Instal dependencies
Here you have debian packages you can install with sudo apt-get install
Find equivalent packages for others distributions:
subversion build-essential automake libtool \
libboost1.54-all-dev zlib1g-dev swig \
openjdk-7-jdk python-all-dev

mkdir mm/
cd mm/

# Save directory path

# Get ImageJ (use it even if you already have another copy of ImageJ or Fiji)

# Retrieve MM source code (can be long)
svn co]( micro-manager1.4
svn co](

# Build MM
cd micro-manager/

# Need to be run two time
./ ; ./

./configure --prefix=$MM_DIR/ImageJ --with-imagej=$MM_DIR/ImageJ --enable-python

# Build binaries (can take a while)

# Install MM libs
make install

# Post install stuff
cp bindist/any-platform/MMConfig_demo.cfg $MM_DIR/ImageJ
echo 'macro "AutoRun" {
  run("Micro-Manager Studio");
}' >> $MM_DIR/ImageJ/macros/StartupMacros.txt

# Write start MM script
cd $MM_DIR/ImageJ

# Create
echo '#!/bin/sh

TOOLS_JAR_PATH=$(find /usr -name tools.jar)

export CLASSPATH=$IJ_PATH/plugins/Micro-Manager

java -mx4000m \
     -Djava.library.path=$IJ_LIB \
     -Dplugins.dir=$IJ_PATH \
     -cp ij.jar:$TOOLS_JAR_PATH \
' >

chmod +x

# Run MM from ImageJ folder
# ./
© Micro-Manager : Vale Lab, UCSF 2006-2011 | All Rights Reserved | Contact