ashesh-0 / pymmcore

Python bindings for MMCore, Micro-Manager's device control layer

pymmcore: Python bindings for MMCore

The pymmcore package provides Python 3.x bindings to Micro-Manager's MMCore (the low-level device control/acquisition interface).

Using pymmcore, you can control and acquire images from all of the microscope devices supported by Micro-Manager, but without the GUI application.

Not to be confused with pycro-manager, which allows control of the entire Micro-Manager application, including its Java APIs, and more.

You might also be interested in pymmcore-plus which wraps this library and provides extra functionality.

Note: pymmcore is similar to the legacy MMCorePy module (Python 2.x only), previously distributed with the Micro-Manager application. However, the Python package for pymmcore is named pymmcore instead of MMCorePy. This is in part to avoid importing the wrong package on systems where pymmcore (usually installed via pip) and MMCorePy (installed with the Micro-Manager app or built by the user) both exist.

Because pymmcore is distributed separately from Micro-Manager, it needs to be "pointed" at an existing Micro-Manager installation to access device adapters. (See the example below.)

Installing

Windows (Python 3.7-3.11), macOS (Python 3.7-3.11, 64-bit), and Linux (Python 3.7-3.11) are supported. Only 64-bit is supported for Python 3.10 and later.

python -m pip install --user pymmcore

You can leave out the --user if installing into a virtual environment (recommended).

Or install via conda:

conda install -c conda-forge pymmcore

Installation by pip should use binary wheels. If pip falls back to building from source code, it will probably fail. If this happens in a supported environment, please file a bug. To manually build from source, the scripts in .github/workflows should serve as a starting point.

You also need a working installation of the Micro-Manager application.

Quick example

import pymmcore
import os.path

mm_dir = "C:/Program Files/Micro-Manager-2.0.x"

mmc = pymmcore.CMMCore()
mmc.setDeviceAdapterSearchPaths([mm_dir])
mmc.loadSystemConfiguration(os.path.join(mm_dir, "MMConfig_demo.cfg"))

mmc.snapImage()
mmc.getImage()

We do not currently have Python-specific documentation for MMCore. The Java documentation is probably the best resource (start at the class CMMCore). There is also C++ documentation.

Matching Micro-Manager and pymmcore versions

The version number of pymmcore is independent of the Micro-Manager version number; instead it tracks the MMCore and device interface versions.

In order to use a given Micro-Manager installation, the device interface version must match between pymmcore and the Micro-Manager device adapters (mmgr_dal_*.dll on Windows).

The device interface version of a given Micro-Manager installation can be viewed in Help > About Micro-Manager.

The device interface version of a given pymmcore version is the fourth part in the version number, and can also be viewed as follows:

import pymmcore
pymmcore.CMMCore().getAPIVersionInfo()

Note that getAPIVersionInfo() should not be confused with getVersionInfo(), which returns the version number of MMCore. (The MMCore version is the first 3 parts of the pymmcore version.)

• For example, pymmcore 10.1.1.69.0 is based on MMCore 10.1.1 and has device interface version 69.
• The device interface version can change independently of the MMCore version, although it is less common for the device interface version to be incremented without a corresponding version change of MMCore.
• Older versions of pymmcore did not include the device interface version in their version number.

For a list of device interface versions for each pymmcore version, see the Releases page.

Loading device adapters on Windows

The majority of device adapters should load once setDeviceAdapterSearchPaths() has been called with the correct directories, as in the above example. However, you may have trouble with device adapters that in turn depend on external DLLs (typically equipment vendor libraries).

To fix this, first ensure that the Micro-Manager application can correctly load all the devices using the same configuration file. Then, use one of the following:

• Temporarily change the current directory to the Micro-Manager installation when loading the configuration file (use os.chdir()).

• Add the Micro-Manager directory to the PATH environment variable.

The first method mimics how the Micro-Manager application works (it always run with the current directory set to the installation directory). However, the second method may be more robust in case the external DLLs in turn load additional DLLs at a later time.

Please report any cases where the Micro-Manager application can load a configuration but pymmcore cannot, even when using the above methods.

Code of Conduct

This project is covered by the Micro-Manager Code of Conduct.

License

The license for pymmcore itself is LGPL 2.1 (see LICENSE.txt). The MMCore component of Micro-Manager (which gets built into pymmcore) is also under the same license. Other parts of Micro-Manager are under different licenses.