Computer Control of Microscopes Using µManager

Arthur Edelstein1, Nenad Amodaj2, Karl Hoover1, Ron Vale3, Nico Stuurman3

1 Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, 2 100x Imaging, San Francisco, California, 3 Howard Hughes Medical Institute, Chevy Chase, Maryland
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 14.20
DOI:  10.1002/0471142727.mb1420s92
Online Posting Date:  October, 2010
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

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. Curr. Protoc. Mol. Biol. 92:14.20.1‐14.20.17. © 2010 by John Wiley & Sons, Inc.

Keywords: Micro‐Manager; µManager; microscopy; automation; open source; cross platform; ImageJ; digital imaging; fluorescence microscopy; multi‐dimensional acquisition

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Basic Protocol 1: Getting Started with µManager
  • Basic Protocol 2: Working with Devices, Properties, and Configuration Settings
  • Basic Protocol 3: Running a Multi‐Dimensional Acquisition
  • Basic Protocol 4: Using the µManager Image Viewer
  • Basic Protocol 5: Connecting and Configuring Hardware
  • Basic Protocol 6: Calibrating Pixel Size
  • Basic Protocol 7: Writing and Running µManager Scripts
  • Basic Protocol 8: Using External Programming Languages to Control µManager
  • Commentary
  • Literature Cited
  • Figures
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

Basic Protocol 1: Getting Started with µManager

  Materials
  • Optional: calibration slide, available from many suppliers. These slides typically bear a photo‐etched calibration grid on one surface. Many variations exist (for instance: Electron Microscopy Sciences 68045‐29); be sure that the distance between the center of the lines of the repeating pattern is known (10 µm for the EMS 68045‐29).
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

   Stuurman, N., Amodaj, N., and Vale, R.D. 2007. Micro‐Manager: Open source software for light microscope imaging. Microsc. Today 15:42‐43.
Internet Resources
  http://micro‐manager.org
  The µManager Web site contains further documentation, download links, and links to a µManager news group through which you can obtain community support.
  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.
  http://beanshell.org
  Beanshell is a Java‐like scripting language used in the µManager script panel.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library