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. 2014;1(2):e10.
doi: 10.14440/jbm.2014.36.

Advanced methods of microscope control using μManager software

Arthur D Edelstein  1 , Mark A Tsuchida  1 , Nenad Amodaj  2 , Henry Pinkard  3 , Ronald D Vale  4 , Nico Stuurman  4
Affiliations

Advanced methods of microscope control using μManager software

Arthur D Edelstein et al. J Biol Methods. 2014.

Abstract

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.

PubMed Disclaimer

Conflict of interest statement

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

Figures

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.
See this image and copyright information in PMC

References

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    1. Devices supported in μManager. Micro-Manager team in Ron Vale lab, Dept. of Cellular and Mol. Pharm. University of California; San Francisco: Cited on August 18, 2014. http://micro-manager.org/wiki/DeviceSupport.
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