Build on MacOS X
first of all, install the current µManager from http://micro-manager.org/downloads.php put it into a directory like /Applications/Micro-Manger1.3 for example this will install ImageJ for use below
cd
...IF you have access to a proprietary section of the the source repository, check it out explicitly thus:
mkdir projects
cd projects
svn checkout https://valelab.ucsf.edu/svn/micromanager2/branches/micromanager1.3
cd micromanager1.3
svn --username YOURNAME --password YOURPASSWORD checkout https://valelab.ucsf.edu/svn/micromanager2/branches/micromanager1.3/SecretDeviceAdapters
continuing:
autoreconf -i -s --force
...now tell the configurator where the ImageJ jar and plugin directory is:
./configure --with-imagej=/Applications/Micro-Manager1.3/ make make install