Micro-Manager is an Open Source software package for imaging and control of automated microscopes on multiple platforms (Windows, Mac and Linux).
Together with ImageJ, a popular image processing package, μManager provides a comprehensive imaging solution – comparable to commercially available ones.
For a tutorial introduction for using Micro-Manager software you've just downloaded, or to get an overview of its basic capabilities 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. Configuration Guide explains how to write new, edit existing configuration files and how to troubleshoot configuration related run-time errors.
Micro-Manager software is designed to strictly separate 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-enable scripting environment such as Matlab. In other words, you can bypass its default, user interface and create your own, either in C++ or Java, or just write scripts in Matlab, or some other compatible environment. 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.