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μManager - Open Source Standard Software for Microscope Automation


Micromanager is an open source ImageJ plug-in which automates image acquisition on a broad range of light microscopy platforms. It is an on-going project of Ron Vale's Lab in the Department of Cellular and Molecular Pharmacology at the University of California, San Francisco. Major vendor's fluorescence and bright field microscopes, focus and stage drives, digital cameras, illumination sources, shutters, filter wheels, hardware autofocus and other peripherals are supported in a flexible cross-platform software system. This automation system orchestrates the function of all these components for the precise and repeatable illumination and imaging of samples. Applications such as automated multi-dimensional image acquisition, software autofocus, slide exploring are built on this framework in a hardware independent fashion. We will detail the current capabilities of Micro-manager, demonstrate the fundamentals of operation of the software, such as how to define acquisition channels, and describe on-going and future plans of the project.


microscope, open-source, acquisition, automation, light

Administrative data

Presenting author: Karl Hoover
Organisation: Vale Lab, UCSF

co-authors: Arthur Edelstein, Nico Stuurman

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