Controlling Micro-Magellan

In addition to launching Micro-Magellan Acquisitions, other aspects of Micro-Magellan can be controlled programatically through Python.

For example, Magellan acquisitions can be created or removed, and have their setting changed:

from pycromanager import Bridge

bridge = Bridge()
#get object representing micro-magellan API
magellan = bridge.get_magellan()

#get the first acquisition appearing in the magellan acquisitions list
acq_settings = magellan.get_acquisition_settings(0)

#add a new one to the list
magellan.create_acquisition_settings()
#remove the one you just added
magellan.remove_acquisition_settings(1)


#Edit the acquisition's settings (i.e. same thing as the controls in the magellan GUI)
#Below is a comprhensive list of all possible settings that be changed. In practice
#only a subset of them will need to be explicitly called

#saving name and path
acq_settings.set_acquisition_name('experiment_1')
acq_settings.set_saving_dir('{}path{}to{}dir'.format(os.sep, os.sep, os.sep))
acq_settings.set_tile_overlap_percent(5)

#time settings
acq_settings.set_time_enabled(True)
acq_settings.set_time_interval(9.1, 's') # 'ms', 's', or 'min'
acq_settings.set_num_time_points(20)

#channel settings
acq_settings.set_channel_group('Channel')
acq_settings.set_use_channel('DAPI', False) #channel_name, use
acq_settings.set_channel_exposure('DAPI', 5.0) #channel_name, exposure in ms
acq_settings.set_channel_z_offset('DAPI', -0.5) #channel_name, offset in um

#space settings
# '3d_cuboid', '3d_between_surfaces', '3d_distance_from_surface', '2d_flat', '2d_surface'
acq_settings.set_acquisition_space_type('3d_cuboid')
acq_settings.set_xy_position_source('New Surface 1')
acq_settings.set_z_step(4.5)
acq_settings.set_surface('New Surface 1')
acq_settings.set_bottom_surface('New Surface 1')
acq_settings.set_top_surface('New Surface 1')
acq_settings.set_z_start(4.1)
acq_settings.set_z_end(10.1)

It is also possible to create Grids for acquisition:

magellan = bridge.get_magellan()

#create 3x3 grid centered at 0.0 stage coordinates
magellan.create_grid('New_grid', 3, 3, 0.0, 0.0)

#delete it (and anything else)
magellan.delete_all_grids_and_surfaces()

Or surfaces:

magellan = bridge.get_magellan()

test_surface = magellan.create_surface('Test surface')

#Use the magellan GUI to add interpolation points

#get the z position of the surface at this XY location
z_position = test_surface.get_extrapolated_value(5., 200.)