Modern light microscopes use digital cameras, motorized stages, shutters, filter wheels, etc., that need to be controlled by computer software. Various commercial solutions exists, all of which have shortfalls. The ?Manager software application is open source, freely available software for microscope automation written for and by scientists that runs on Windows, Mac OS X, and Linux. It provides an easy-to-use interface through which most microscope hardware can be controlled making it simple for scientists to carry out experiments using equipment from different vendors. The software is used at about 2000 microscopes world-wide, and provides significant savings to the NIH since individual copies of commercial alternatives cost $5-15k. ?Manager also provides a hardware abstraction layer that is used by scientists with programming abilities to automate their microscope hardware in novel and creative ways. The open source nature of this project not only makes it possible to see exactly how acquisition protocols are carried out (which is important in research), but also attracts many code contributions from industry and academia. Many companies already make sure that their equipment works within ?Manager and maintain the source code for their equipment in the ?Manager source code repository. More than 50 programmers have contributed code, a number that continues to rise. This grant will be used to continue stewardship of these many code contributions, regularly release user-friendly installers for the software, improve documentation, address bug reports, etc. It will also be used to add novel capabilities to the software such as live STORM/PALM imaging, structured illumination-based optical sectioning, and photo-bleaching/photo-activation using digital mirror devices. In addition, integration with existing open source microscopy-related software packages will be improved.

Public Health Relevance

This project develops and maintains ?Manager, the world's only comprehensive open source software package for microscope automation. Available for free download, ?Manager provides a substantial cost savings for NIH and encourages the application of novel, innovative techniques in light microscopy. ?Manager software is used to control a growing number of microscopes (currently >2,000) world-wide.

National Institute of Health (NIH)
National Institute of Biomedical Imaging and Bioengineering (NIBIB)
Research Project (R01)
Project #
Application #
Study Section
Enabling Bioanalytical and Imaging Technologies Study Section (EBIT)
Program Officer
Pai, Vinay Manjunath
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Francisco
Schools of Medicine
San Francisco
United States
Zip Code
Carbone, Catherine B; Kern, Nadja; Fernandes, Ricardo A et al. (2017) In vitro reconstitution of T cell receptor-mediated segregation of the CD45 phosphatase. Proc Natl Acad Sci U S A 114:E9338-E9345
Carbone, Catherine B; Vale, Ronald D; Stuurman, Nico (2016) An acquisition and analysis pipeline for scanning angle interference microscopy. Nat Methods 13:897-898
Stuurman, Nico; Vale, Ronald D (2016) Impact of New Camera Technologies on Discoveries in Cell Biology. Biol Bull 231:5-13
Pinkard, Henry; Stuurman, Nico; Corbin, Kaitlin et al. (2016) Micro-Magellan: open-source, sample-adaptive, acquisition software for optical microscopy. Nat Methods 13:807-809
Edelstein, Arthur D; Tsuchida, Mark A; Amodaj, Nenad et al. (2014) Advanced methods of microscope control using ?Manager software. J Biol Methods 1:
Conrad, Christian; W├╝nsche, Annelie; Tan, Tze Heng et al. (2011) Micropilot: automation of fluorescence microscopy-based imaging for systems biology. Nat Methods 8:246-9
Edelstein, Arthur; Amodaj, Nenad; Hoover, Karl et al. (2010) Computer control of microscopes using ┬ÁManager. Curr Protoc Mol Biol Chapter 14:Unit14.20