Flexible, open source software for laser scanning microscopy

Northwestern University At Chicago, Evanston IL

Investigators

Linked publications & trials

Abstract

(Cl.) Laser scanning microscopy (LSM), including confocal and 2-photon microscopy, continues to play a central role in many areas of biomedical research. In neuroscience alone, the number of applications continues to grow rapidly. However, in contrast to the ongoing advances made on the hardware aspects of LSM (eg. improved, cheaper light sources, detectors, and scanners), a major limitation to using LSM continues to be the cost and inflexibility of commercial software. Several years ago we introduced Scanlmage, an open source software package for LSM. Scanlmage has been highly successful and is now used by many labs, in particular for 2-photon microscopy. However, new types of cutting-edge applications require new functionality. In addition, it is usually important to combine LSM with other types of digital or analog stimulation or acquisition, such as electrophysiology, underscoring a related, more fundamental need, for an open-source general-purpose data acquisition program. Here, we propose (1) to continue to develop Scanlmage, with a focus on in vivo imaging and (2) to develop Ephus, a new and complementary program for general-purpose laser scanning and data acquisition, such as electrophysiological recording and video imaging. These programs are mostly written in Matlab, with an underlying C-backbone. Future releases of Scanimage will support new types of scanning hardware;improved region-of-interest and related scans;fast z-scanning;and, improved on-line multicolor display. Future releases of Ephus will include support for COD camera -based image acquisition and tools to facilitate easy creation of complex experimental paradigms, such as laser scanning photostimulation based mapping of neural circuits, We will maintain wiki-style documentation for Scanimage and Ephus. We believe that Scanlmage/Ephus will facilitate exciting biological discovery in numerous laboratories. v0, 0-0 0(Q --[unreadable] CAA N-0 .t? ,-,. .(D (n[unreadable] 0--u 6-0 aim ..c 11) (1) +-. (cu 07M O-> mom