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pymmcore-plus · GitHub

Tools for using Micro-Manager in a pure-python environment

This organization contains a number of packages that work together (in conjunction with pymmcore) to control microscopes in a pure python/C environment (i.e. with no Java dependency or cross-process runtime).

The diagram below attempts to clarify how many libraries and components that have been built around the micro-manager ecosystem relate to each other.

• 📦 pymmcore-plus - a drop in super-set of pymmcore.CMMCore. Adds a pure-python multi-dimensional acquisition engine (analogous to AcqEngineJ and the clojure acqEngine); a more robust event/signaling system for monitoring the state of MMCore; many additional convenience functions and structures; and an improved python developer experience (typing, docstrings, etc...)
• 📦 useq-schema - an implementation agnostic schema for a sequence of events during a multi-dimensional imaging acquisition. Written in python, but language agnostic and exported as JSONschema. It is essentially just a specification for how to describe a microscopy experiment declaratively in, for example, a JSON or YAML file, or in python dataclasses. The pymmcore_plus.CMMCorePlus.mda.run method accepts an instance of a useq.MDASequence object (or any iterable of useq.MDAEvent objects) as an input, but conceptually, any microscope control system (independent of micro-manager) could implement support for MDASequence.
• 📦 pymmcore-widgets - a set of Qt-based widgets, each of which provide GUI-based readout and control of certain components controlled by an underlying pymmcore_plus.CMMCorePlus instance (for example, a shutter widget, a stage controller, or a multi-dimensional acquisition builder).
• 🖥️ pymmcore-gui - Complete GUI application for pymmcore-plus. This is an alternative to napari-micromanager: it uses ndv instead of napari. It is designed as a complete "double-clickable" desktop application (a replacement for the Java-Based Micro-Manager application called MMStudio).
• napari-micromanager - a high-level plugin for napari. It uses all of the packages listed above, and composes widgets from pymmcore-widgets into a complete GUI capable of running a microscope and showing the collected images in a multidimensional viewer.
• pymmcore-nano - Experimental python bindings for CMMCore using nanobind. This is an alternative to pymmcore, which uses SWIG. pymmcore-plus supports both pymmcore and pymmcore-nano, and will use nano if present.

• MMCore (and devices) - C++ core of micro-manager. This is the heart of micro-manager. It's what actually manages and communicates with microscope devices.
• pymmcore - thin python wrapper around mmCoreAndDevices
• MMCoreJ - The Java wrapper around mmCoreAndDevices
• Pycro-manager - python library that can control the Java micro-manager application via inter-process communication.
• PycroManagerJava - the Java half of Pycro-manager: a ZMQ server that communicates with the Python client as well as mmstudio and the Java-based acquisition engine
• MMStudio - the Java-based micro-manager GUI application.
• clojure acqEngine - original acquisition engine (written in clojure and used by MMStudio): this is the bit that has conventionally driven the microscope during an MDA acquisition.
• AcqEngJ - A Java-based alternative engine to the clojure one, originally written for MicroMagellan and Pycro-manager, but being integrated into the Java based MMStudio
• napari - multidimensional data viewer in Python.

1. GUI interface between napari and micromanager powered by pymmcore-plus and pymmcore-widgets

   Python 70 23

2. Pure python/C++ micro-manager ecosystem

   Python 41 17

3. An implementation agnostic schema for describing a sequence of events during a multi-dimensional imaging acquisition.

   Python 19 8

4. A set of Qt-based widgets onto the pymmcore-plus model

   Python 17 9

5. Pure Python Micro-Manager GUI Application, built on pymmcore-plus

   Python 14 6

• pymmcore-plus/setup-mm-test-adapters’s past year of commit activity Makefile 0 0 0 0 Updated Aug 17, 2025
• pymmcore-plus/mm-test-adapters’s past year of commit activity Meson 0 2 0 0 Updated Aug 17, 2025
• pymmcore-nano Public

  Python bindings for CMMCore (micro-manager) using nanobind instead of SWIG

  pymmcore-plus/pymmcore-nano’s past year of commit activity C++ 2 LGPL-2.1 2 0 2 Updated Aug 16, 2025
• pymmcore-plus/pymmcore-plus’s past year of commit activity Python 41 BSD-3-Clause 17 24 8 Updated Aug 16, 2025
• useq-schema Public

  An implementation agnostic schema for describing a sequence of events during a multi-dimensional imaging acquisition.

  pymmcore-plus/useq-schema’s past year of commit activity Python 19 BSD-3-Clause 8 8 4 Updated Aug 15, 2025
• pymmcore-plus/pymmcore-widgets’s past year of commit activity Python 17 9 17 6 Updated Aug 15, 2025
• pymmcore-remote Public

  Communicate remotely with a pymmcore-plus core instance

  pymmcore-plus/pymmcore-remote’s past year of commit activity Python 2 BSD-3-Clause 2 3 2 Updated Aug 11, 2025
• napari-micromanager Public

  GUI interface between napari and micromanager powered by pymmcore-plus and pymmcore-widgets

  pymmcore-plus/napari-micromanager’s past year of commit activity Python 70 BSD-3-Clause 23 15 4 Updated Aug 4, 2025
• pymmcore-midi Public

  MIDI Device control for microscopes using pymmcore

  pymmcore-plus/pymmcore-midi’s past year of commit activity Python 1 BSD-3-Clause 1 0 3 Updated Aug 4, 2025
• pymmcore-plus/.github’s past year of commit activity 0 0 0 0 Updated Jul 7, 2025

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