pymmcore-plus

pymmcore-plus extends pymmcore (python bindings for the C++ micro-manager core) with a number of features designed to facilitate working with Micro-manager in pure python/C environments.

pymmcore_plus.CMMCorePlus is a drop-in replacement subclass of pymmcore.CMMCore that provides a number of helpful overrides and additional convenience functions beyond the standard CMMCore API. See CMMCorePlus documentation for details.
CMMCorePlus includes a run_mda method (name may change) "acquisition engine" that drives micro-manager for conventional multi-dimensional experiments. It accepts an MDASequence from useq-schema for experiment design/declaration.
Adds a callback system that adapts the CMMCore callback object to an existing python event loop (such as Qt, or perhaps asyncio/etc...). The CMMCorePlus class also fixes a number of "missed" events that are not currently emitted by the CMMCore API.

Documentation

https://pymmcore-plus.github.io/pymmcore-plus/

Why not just use `pymmcore` directly?

pymmcore is (and should probably remain) a thin SWIG wrapper for the C++ code at the core of the Micro-Manager project. It is sufficient to control micromanager via python, but lacks some "niceties" that python users are accustomed to. This library:

extends the pymmcore.CMMCore object with additional methods
fixes emission of a number of events in MMCore.
provide proper python interfaces for various objects like Configuration and Metadata.
provides an object-oriented API for Devices and their properties.
uses more interpretable Enums rather than int for various constants
improves docstrings and type annotations.
generally feel more pythonic (note however, camelCase method names from the CMMCore API are not substituted with snake_case).

What about `Pycro-Manager`?

Pycro-Manager is a library designed to make it easier to work with and control the Java Micro-manager application using python. As such, it requires Java to be installed and running in the background (either via the micro-manager GUI application directly, or via a headless process). The python half communicates with the Java half using ZeroMQ messaging.

In brief: while Pycro-Manager provides a python API to control the Java Micro-manager application (which in turn controls the C++ core), pymmcore-plus provides a python API to control the C++ core directly, without the need for Java in the loop.

Quickstart

Install

# from pip
pip install pymmcore-plus

# from conda
conda install -c conda-forge pymmcore-plus

# or from source tree
pip install git+https://github.com/pymmcore-plus/pymmcore-plus.git

Usually, you'll then want to install the device adapters (though you can also download these manually from micro-manager.org):

mmcore install

See installation documentation for more details.

Usage

Then use the core object as you would pymmcore.CMMCore... but with more features 😄

from pymmcore_plus import CMMCorePlus

core = CMMCorePlus()
...

Examples

See a number of usage examples in the documentation.

You can find some basic python scripts in the examples directory of this repository

Contributing

Contributions are welcome! See contributing guide.

jqwhite/pymmcore-plus