Advanced methods of microscope control using μManager software

Authors

  • Arthur D Edelstein
  • Mark A Tsuchida University of California, San Francisco
  • Nenad Amodaj Luminous Point, LLC
  • Henry Pinkard University of California, San Francisco
  • Ronald D Vale University of California, San Francisco / Howard Hughes Medical Institute
  • Nico Stuurman University of California, San Francisco / Howard Hughes Medical Institute

DOI:

https://doi.org/10.14440/jbm.2014.36

Keywords:

high-speed imaging, high-content screening, localization microscopy, Micro-Manager, open-source microscopy

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.

References

ImageJ website. Wayne Rasband, NIH. Cited on August 18, 2014. http://imagej.nih.gov/ij

Micro-Manager website. 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.

Edelstein, A., Amodaj, N., Hoover, K., Vale, R., & Stuurman, N. (2010) Computer control of microscopes using µManager. Current protocols in molecular biology, 14-20.

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/Device Support

ImageJ plugin GridAligner. Nico Stuurman in Ron Vale Lab, Dept. of Cellular and Mol. Pharm., University of California San Francisco. Cited on August 18, 2014. http://valelab.ucsf.edu/~nstuurman/IJplugins/GridAligner.html

Tomer, R., Khairy, K., Amat, F., & Keller, P. J. (2012) Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nature Methods, 9(7), 755-763.

Huang, Z. L., Zhu, H., Long, F., Ma, H., Qin, L., Liu, Y., & Zeng, S. (2011) Localization-based super-resolution microscopy with an sCMOS camera.Optics express, 19(20), 19156-19168.

Instructions and scripts to measure camera specifications. Nico Stuurman on the Micro-Manager website, Ron Vale Lab, Dept. of Cellular and Mol. Pharm., University of California San Francisco. Cited on August 18, 2014. http://micro-manager.org/wiki/Measuring_camera_specifications.

Description of the Tagged Spot Format. Nico Stuurman on the Micro-Manager website, Ron Vale Lab, Dept. of Cellular and Mol. Pharm., University of California San Francisco. Cited on August 18, 2014. http://micro-manager.org/wiki/Tagged_Spot_File_%28tsf%29_format.

Goshtasby, A. (1988). Image registration by local approximation methods. Image and Vision Computing, 6(4), 255-261.

Huang, B., Wang, W., Bates, M., & Zhuang, X. (2008) Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy.Science, 319(5864), 810-813.

Diagnostic slides from Chroma. Chroma Technology Corp. Cited on August 18, 2014. http://www.chroma.com/products/filter-accessories/diagnostic-slides.

Micro-Manager mailing list. Sourceforge. Cited on August 18, 2014. https://lists.sourceforge.net/lists/listinfo/micro-manager-general

Downloads

Published

2014-11-07

How to Cite

1.
Edelstein AD, Tsuchida MA, Amodaj N, Pinkard H, Vale RD, Stuurman N. Advanced methods of microscope control using μManager software. J Biol Methods [Internet]. 2014Nov.7 [cited 2021Sep.21];1(2):e10. Available from: https://jbmethods.org/jbm/article/view/36

Issue

Section

Protocols