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FocusStack and StimServer: a new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data

Muir, Dylan R. and Kampa, Björn M.. (2014) FocusStack and StimServer: a new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data. Frontiers in neuroinformatics, 8. p. 85.

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Abstract

Two-photon calcium imaging of neuronal responses is an increasingly accessible technology for probing population responses in cortex at single cell resolution, and with reasonable and improving temporal resolution. However, analysis of two-photon data is usually performed using ad-hoc solutions. To date, no publicly available software exists for straightforward analysis of stimulus-triggered two-photon imaging experiments. In addition, the increasing data rates of two-photon acquisition systems imply increasing cost of computing hardware required for in-memory analysis. Here we present a Matlab toolbox, FocusStack, for simple and efficient analysis of two-photon calcium imaging stacks on consumer-level hardware, with minimal memory footprint. We also present a Matlab toolbox, StimServer, for generation and sequencing of visual stimuli, designed to be triggered over a network link from a two-photon acquisition system. FocusStack is compatible out of the box with several existing two-photon acquisition systems, and is simple to adapt to arbitrary binary file formats. Analysis tools such as stack alignment for movement correction, automated cell detection and peri-stimulus time histograms are already provided, and further tools can be easily incorporated. Both packages are available as publicly-accessible source-code repositories.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Former Organization Units Biozentrum > Neural Networks (Mrsic-Flogel)
UniBasel Contributors:Muir, Dylan R
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Frontiers Media
ISSN:1662-5196
Note:Publication type according to Uni Basel Research Database: Journal article -- This Document is Protected by copyright and was first published by Frontiers. All rights reserved. It is reproduced with permission.
Language:English
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Last Modified:16 Aug 2016 14:05
Deposited On:16 Aug 2016 14:04

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