Run the Micro Manager from the terminal with a configuration file as input argument or from a Python script.

The Micro Manager is run directly from the terminal by providing the path to the configuration file as an input argument in the following way

micro_manager micro-manager-config.json

Alternatively the Manager can also be run by creating a Python script which imports the Micro Manager package and calls its run function. For example a run script would look like

from micro_manager import MicroManager

manager = MicroManager("micro-manager-config.json")


The Micro Manager can also be run in parallel, using the same script as stated above

mpirun -n <number-of-procs> python3