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BioMedical Engineering OnLine

, 2:13

First Online: 17 May 2003Received: 09 February 2003Accepted: 17 May 2003


BackgroundLaser 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.

ResultsWe 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.

ConclusionsWe present ScanImage, software to run a flexible laser scanning microscope that allows easy custom design.

List of Abbreviations2PLSMtwo-photon excitation laser scanning microscopy

CLSMconfocal laser scanning microscopy

DAQdata acquisition

CPUcentral processing unit

TTLtransistor-transistor logic

PMTphoto-multiplier tube

GUIgraphical user interface


LUTlook-up table

DSPdigital signal processing

COMcommunications port


SEMstandard error of the mean

RAMrandom access memory

Electronic supplementary materialThe online version of this article doi:10.1186-1475-925X-2-13 contains supplementary material, which is available to authorized users.

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Autor: Thomas A Pologruto - Bernardo L Sabatini - Karel Svoboda


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