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Advanced Methods of Microscope Control Using μManager Software


Advanced Methods of Microscope Control Using μManager Software

Arthur D Edelstein et al. J Biol Methods.


μManager is an open-source, cross-platform desktop application, to control a wide variety of motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories. Since its inception in 2005, μManager has grown to support a wide range of microscopy hardware and is now used by thousands of researchers around the world. The application provides a mature graphical user interface and offers open programming interfaces to facilitate plugins and scripts. Here, we present a guide to using some of the recently added advanced μManager features, including hardware synchronization, simultaneous use of multiple cameras, projection of patterned light onto a specimen, live slide mapping, imaging with multi-well plates, particle localization and tracking, and high-speed imaging.

Keywords: Micro-Manager; high-content screening; high-speed imaging; localization microscopy; open-source microscopy.

Conflict of interest statement

Competing interests: A.D.E. is now self-employed and provides Micro-Manager related programming services.


Figure 1
Figure 1
The HCS Site Generator plugin provides a simple user interface to generate XY positions for a multi-well plate for imaging with μManager’s Multi-Dimensional Acquisition.
Figure 2
Figure 2. The Slide Explorer plugin allows a large image to be synthesized by a grid of tiled images
On the left is a mosaic image of a mouse kidney section imaged in three fluorescent channels. On the right is a zoomed-in portion of the mosaic image.
Figure 3
Figure 3. The main window for the Localization Microscopy plugin
Edit settings in this window to control the algorithms for localization and tracking of particles in an image series.

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