For a tutorial introduction for using Micro-Manager software you’ve just downloaded, or to get an overview of its basic capabilities, the User’s Guide is the best starting point. Here you’ll find out how to navigate through the application’s menus and dialogs and how to perform basic instrument control and acquisition. The User’s Guide assumes you are running the software either in the “demo” mode (installation default), or that you are working with a previously configured hardware setup.
Configuring Micro-Manager software to work with your particular hardware setup is a separate topic, covered in detail in the Configuration Guide. Micro-Manager uses configuration files in textual, human-readable form to load appropriate device drivers and to adapt user interface to particular properties of your hardware setup. The Configuration Guide explains how to write new configuration files, how to edit existing ones, and how to troubleshoot configuration-related run-time errors.
Micro-Manager software is designed to strictly separate the user interface from the functional core module. That means that you can use its comprehensive set of microscope control and image acquisition commands from any Java program or Java-enabled scripting environment, such as Matlab. In other words, you can bypass Micro-Manager’s default, user interface and create your own, either in C++ or Java, or just write scripts in Matlab, or some other compatible environment. The Programming Guide describes how to use the Micro-Manager programmatic interface (API) and demonstrates how to control the microscope setup from Java/C++ program or from the scripting environment. The entire API is listed in the API Reference in auto-generated Doxygen format. Device adapter authors will be intersted in the Device-API reference.