control_core.py

"""
This example shows how to use pycromanager to interact with the micro-manager core.
Aside from the setup section, each following section can be run independently
"""
from pycromanager import _Bridge, ZMQRemoteMMCoreJ
import numpy as np
import matplotlib.pyplot as plt

#### Setup ####
# establish communication with Magellan
with _Bridge() as bridge:
    # get object representing micro-manager core
    core = bridge.get_core()


    #### Calling core functions ###
    exposure = core.get_exposure()


    #### Setting and getting properties ####
    # Here we set a property of the core itself, but same code works for device properties
    auto_shutter = core.get_property("Core", "AutoShutter")
    core.set_property("Core", "AutoShutter", 0)


    #### Acquiring images ####
    # The micro-manager core exposes several mechanisms foor acquiring images. In order to
    # not interfere with other pycromanager functionality, this is the one that should be used
    core.snap_image()
    tagged_image = core.get_tagged_image()
    # If using micro-manager multi-camera adapter, use core.getTaggedImage(i), where i is
    # the camera index

# pixels by default come out as a 1D array. We can reshape them into an image
pixels = np.reshape(
    tagged_image.pix, newshape=[tagged_image.tags["Height"], tagged_image.tags["Width"]]
)
# plot it
plt.imshow(pixels, cmap="gray")
plt.show()