title: ScanImage: flexible software for operating laser scanning microscopes.
abstract: BACKGROUND
  Laser scanning microscopy is a powerful tool for analyzing the structure and function of biological specimens. Although numerous commercial laser scanning microscopes exist, some of the more interesting and challenging applications demand custom design. A major impediment to custom design is the difficulty of building custom data acquisition hardware and writing the complex software required to run the laser scanning microscope.
  
  
  RESULTS
  We describe a simple, software-based approach to operating a laser scanning microscope without the need for custom data acquisition hardware. Data acquisition and control of laser scanning are achieved through standard data acquisition boards. The entire burden of signal integration and image processing is placed on the CPU of the computer. We quantitate the effectiveness of our data acquisition and signal conditioning algorithm under a variety of conditions. We implement our approach in an open source software package (ScanImage) and describe its functionality.
  
  
  CONCLUSIONS
  We present ScanImage, software to run a flexible laser scanning microscope that allows easy custom design.
authors.affiliation: Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA. pologrut@cshl.org;
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Pologruto
authors.forename: Bernardo L
authors.initials: BL
authors.lastname: Sabatini
authors.forename: Karel
authors.initials: K
authors.lastname: Svoboda
mesh_terms: D004867:Equipment Design; D007089:Image Enhancement / Q000379:methods; D018613:Microscopy, Confocal / Q000295:instrumentation*; D012815:Signal Processing, Computer-Assisted; D012984:Software; D012985:Software Design; D014584:User-Computer Interface