ScanImage: Flexible software for operating laser scanning microscopes

TLDR

Laser scanning microscopy is a powerful tool for analyzing biological specimens, yet many challenging applications require custom design beyond existing commercial microscopes. The authors aim to provide a simple, software-based solution that eliminates the need for custom data acquisition hardware to operate a laser scanning microscope. They achieve this by using standard data acquisition boards for control and placing all signal integration and image processing on the computer’s CPU, and they quantify the algorithm’s effectiveness under various conditions. They implemented the approach in the open‑source ScanImage package, demonstrating that it enables flexible laser scanning microscopy and facilitates easy custom design.

Abstract

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