The article introduces μManager, a free and open-source software for controlling automated microscope equipment. μManager offers a universal standard for controlling microscopes, cameras, stages, and other peripheral equipment from various manufacturers, and runs on Windows, Mac, and Linux. It includes an easy-to-use graphical user interface (GUI) and advanced customization tools. The software supports a wide range of hardware, allowing researchers to combine devices of different brands and control them together on a single microscope system. μManager automates complex imaging sequences, making them repeatable and reproducible. The article provides protocols for getting started with μManager, including downloading and installing the software, using the main window, connecting and configuring hardware, calibrating pixel size, writing and running scripts, and using external programming languages like Python and MATLAB. μManager's modular architecture allows for easy addition of new functionality, and its open-source nature makes it accessible for advanced microscopy techniques and low-cost research.The article introduces μManager, a free and open-source software for controlling automated microscope equipment. μManager offers a universal standard for controlling microscopes, cameras, stages, and other peripheral equipment from various manufacturers, and runs on Windows, Mac, and Linux. It includes an easy-to-use graphical user interface (GUI) and advanced customization tools. The software supports a wide range of hardware, allowing researchers to combine devices of different brands and control them together on a single microscope system. μManager automates complex imaging sequences, making them repeatable and reproducible. The article provides protocols for getting started with μManager, including downloading and installing the software, using the main window, connecting and configuring hardware, calibrating pixel size, writing and running scripts, and using external programming languages like Python and MATLAB. μManager's modular architecture allows for easy addition of new functionality, and its open-source nature makes it accessible for advanced microscopy techniques and low-cost research.