Installation:

Setting up the Enviroment:

change to base folder and run 'initialize' to set the paths
to initialize bioformat interface run bfinitialize
to initialize imagej interface run ijinitialize
to initialize hugin interface run hiinitialize
to initialize imaris interface run imarisinitialize

Get Started:

look into the Scripts/Examples folder open a script and run it cell by cell

Compilation:

Some c++ code might not work on your machine: recompile using the compileXXX commands, e.g. for imaris compileImaris etc..