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Using the Micro-Manager python library

Revision as of 17:05, 12 October 2009 by Arthuredelstein (Talk | contribs)

A python wrapper for the Micro-Manager core is available on Mac and Windows, allowing you to control hardware from python scripts or the command line. Currently, the python wrapper does not include the Micro-Manager Java GUI or ImageJ -- instead, only the C++ core can be controlled. After Micro-Manager has been installed on your machine, will be located in the main Micro-Manager directory; it requires many library files in that directory (with suffixes like .dll, .so, .pyd) to operate. To use the MMCorePy library, you will need to install the latest versions of:

You can make the Micro-Manager python wrapper library generally available by adding your micro-manager directory to the PYTHONPATH environment variable.

Images returned by calls to the Micro-Manager core object (CMMCore) are stored in numpy arrays for convenience, and can be easily displayed by pylab (matplotlib) commands. Here is a short example that demonstrates use of the python wrapper to acquire and display an image.

# Create a Micro-Manager core object:
import MMCorePy
mmc = MMCorePy.CMMCore()

#  Load and initialize the demo camera device:

# Snap and retrieve an image:
im1 = mmc.getImage()

# Display the image:
from pylab import *
ion() # Activate interactive mode
imshow(im1,cmap = cm.gray)

A longer example script,, is available in the Micro-Manager root directory.

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