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.

Agency
National Institute of Health (NIH)
Institute
National Institute of Biomedical Imaging and Bioengineering (NIBIB)
Type
Research Project (R01)
Project #
5R01EB007187-06
Application #
8554762
Study Section
Enabling Bioanalytical and Imaging Technologies Study Section (EBIT)
Program Officer
Pai, Vinay Manjunath
Project Start
2007-04-01
Project End
2015-08-31
Budget Start
2013-09-01
Budget End
2014-08-31
Support Year
6
Fiscal Year
2013
Total Cost
$388,478
Indirect Cost
$141,302
Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Medicine
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94143
Conrad, Christian; Wunsche, 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