ScanImage: Flexible software for operating laser scanning microscopes

By T. Pologruto, Bernardo L. Sabatini, Karel Svoboda. BioMedical Engineering OnLine, 2003

1,314 citations recorded by the source corpus.

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.

Subfields: Biophysics, Media Technology

View Paper: https://www.semanticscholar.org/paper/6639b21cc861944e9e71cf8f8f18598052b4c28e

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Citations in the corpus

Fast and sensitive GCaMP calcium indicators for imaging neural populations (2021, neutral): “05) and comparable to 8m (84[32-165] ms) and XCaMP-Gf (91[48-155] ms) (Fig.”
Population-scale organization of cerebellar granule neuron signaling during a visuomotor behavior (2017, methodology): “Signals from the PMTs and the PD were acquired by ScanImage(Pologruto et al., 2003) to generate fluorescence and contrast images of specimen in the focal plane.”
Stereotyped Odor-Evoked Activity in the Mushroom Body of Drosophila Revealed by Green Fluorescent Protein-Based Ca2+ Imaging (2004, methodology): “Microscope control was accomplished using the custom-written software package ScanImage (Pologruto et al., 2003).”
High-Content Screening for Quantitative Cell Biology. (2016, neutral): “scanImage Automation of laser-scanning microscopes [67] http://svobodalab.”
Activity of Defined Mushroom Body Output Neurons Underlies Learned Olfactory Behavior in Drosophila (2015, methodology): “Images of 256 3 128 pixels were acquired at 11.5 Hz using two-photon microscopy (Scientifica) with a 40X, 0.8 NA water-immersion objective, controlled by ScanImage 3.8 software (Pologruto et al., 2003).”
Probing the limits to positional information. (2007, methodology): “Microscope control routines (Pologruto et al., 2003) and all our image analysis routines were implemented in Matlab software (MATLAB, MathWorks, Natick, MA).”