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 run-micro-manager.py would look like
from micro_manager import MicroManager
manager = MicroManager("micro-manager-config.json")
manager.initialize()
manager.solve()
The Micro Manager can also be run in parallel, using the same script as stated above
mpirun -n <number-of-procs> python3 run-micro-manager.py