Overview of the documentation
The following are the three main guides to fully explore Micro-Manager:
User Guide: Here you will find how to navigate through the software's menus, dialogs and also perform basic instrument control and acquisition. The guide assumes you are running the software either in the "demo" mode (default installation), or that you are working with a previously configured hardware setup.
Configuration Guide: In order to get Micro-Manager to work with your particular hardware setup, this guide will cover in detail how 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. You will also see details on how to write new configuration files, edit existing files, and troubleshoot configuration-related run-time errors.
Programming Guide: This 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 other scripting environments. Micro-Manager 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. The entire API is listed in the API Reference in auto-generated Doxygen format. Device adapter authors will be interested in the Device-API reference.