Over the last decade the availability of new laser light sources and modern data acquisition engines has dramatically increased the range of applications of laser scanning microscopy (LSM). Today, LSM includes some of the most important optical imaging modalities in biology, including confocal and 2-photonmicroscopy. LSM is central to research in neurobiology, cancer research, immunology, pathology, developmental biology and other fields of research. Experimental systems amenable to LSM range from single biomolecules to whole living animals. Although numerous commercial LSMs exist, the most interesting and challenging applications of LSM demand custom hardware and software. However, few investigators have attempted this approach, mainly because of the difficulty of writing the complex software required to run a laser scanning microscope. Open source software for laser scanning microscopy is not available. In our laboratory we have developed a powerful program to control a laser scanning microscope. This program, Scanlmage, performs all of the typical functions a LSM performs with important advantages, i) Scanlmage is almost entirely written in Matlab, thereby fusing image acquisition with one of the most sophisticated image analysis environments; ii) Scanlmage uses a novel approach to signal conditioning and integration, and does not require complex custom electronics, removing significant obstacles to custom design; iii) Scanlmage miswritten in a modular and object-oriented style, making it easily expandable to accommodate emerging technologies. We propose to produce on-line help and documentation for Scanlmage and make the software available open source. We further propose to develop new modules for Scanlmage to address the need to integrate LSM with new imaging technologies. These new modules will include random access laser scanning, the simultaneous operation of two scanners (e.g. one for imaging and the other for photolytic release of bioactive substances), and the combination of laser scanning microscopy and fluorescence lifetime imaging. We believe that Scanlmage will facilitate exciting biological discovery in numerous laboratories. ? ?

National Institute of Health (NIH)
National Institute of Biomedical Imaging and Bioengineering (NIBIB)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-SSS-H (91))
Program Officer
Peng, Grace
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Cold Spring Harbor Laboratory
Cold Spring Harbor
United States
Zip Code
Shepherd, Gordon M G (2012) Circuit mapping by ultraviolet uncaging of glutamate. Cold Spring Harb Protoc 2012:998-1004
Suter, Benjamin A; O'Connor, Timothy; Iyer, Vijay et al. (2010) Ephus: multipurpose data acquisition software for neuroscience experiments. Front Neural Circuits 4:100
Pologruto, Thomas A; Sabatini, Bernardo L; Svoboda, Karel (2003) ScanImage: flexible software for operating laser scanning microscopes. Biomed Eng Online 2:13