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. 2010 Oct:Chapter 14:Unit14.20.
doi: 10.1002/0471142727.mb1420s92.

Computer control of microscopes using µManager

Arthur Edelstein  1 , Nenad Amodaj, Karl Hoover, Ron Vale, Nico Stuurman
Affiliations

Computer control of microscopes using µManager

Arthur Edelstein et al. Curr Protoc Mol Biol. 2010 Oct.

Abstract

With the advent of digital cameras and motorization of mechanical components, computer control of microscopes has become increasingly important. Software for microscope image acquisition should not only be easy to use, but also enable and encourage novel approaches. The open-source software package µManager aims to fulfill those goals. This unit provides step-by-step protocols describing how to get started working with µManager, as well as some starting points for advanced use of the software.

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Figures

Figure 1
Figure 1
μManager’s “splash screen” window that appears when the application is started. Use this window to choose a configuration file that contains the hardware settings for your system. A drop down menu lets you select recent configuration files, and the button to its right (…) opens a file browser dialog window where you can choose a new configuration file.
Figure 2
Figure 2
The main μManager window, where the application’s primary controls are located.
Figure 3
Figure 3
The property browser window. To reach it, choose Tools -> Device/Property Browser…. All major hardware properties and their values are included in this table.
Figure 4
Figure 4
The Multi-Dimensional Acquisition window. Use the check-boxes to select which of the five dimensions you want to include in an acquisition: Time points, Multiple positions (XY), Z-stacks (slices), and Channels.
Figure 5
Figure 5
The 5D Image Viewer of μManager. Use the z and t sliders to view different slices and time points; use the boxes at the right to show and hide channels; use the buttons at bottom to save files, halt acquisition, examine metadata, adjust contrast, and play back time lapse sequences.
Figure 6
Figure 6
The Stage-position List window. Manage waypoints in 2 or 3 dimensions in the position list table. Each position can refer to one or more stage axes
Figure 7
Figure 7
The Image Metadata window. Experimental annotations can be entered in the Comment tab.
Figure 8
Figure 8
The Script Window. Scripts are written in Beanshell and allow fine-grained control of all aspects of μManager.
See this image and copyright information in PMC

References

    1. μManager website. http://micro-manager.org. The μManager website contains further documentation, download links, and links to a μManager news group through which you can obtain community support.
    1. ImageJ website. http://rsbweb.nih.gov/ij/ ImageJ is a public domain cross-platform application for image analysis. Hundreds of plugins extend its capabilities. μManager runs as an ImageJ plugin.
    1. Beanshell Documentation. http://beanshell.org Beanshell is a java-like scripting language used in the μManager script panel.

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