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dc.contributor.advisorHan, Xueen_US
dc.contributor.authorBucklin, Mark E.en_US
dc.date.accessioned2019-08-15T17:24:47Z
dc.date.available2019-08-15T17:24:47Z
dc.date.issued2019
dc.identifier.urihttps://hdl.handle.net/2144/37110
dc.description.abstractImaging of multiple cells has rapidly multiplied the rate of data acquisition as well as our knowledge of the complex dynamics within the mammalian brain. The process of data acquisition has been dramatically enhanced with highly affordable, sensitive image sensors enable high-throughput detection of neural activity in intact animals. Genetically encoded calcium sensors deliver a substantial boost in signal strength and in combination with equally critical advances in the size, speed, and sensitivity of image sensors available in scientific cameras enables high-throughput detection of neural activity in behaving animals using traditional wide-field fluorescence microscopy. However, the tremendous increase in data flow presents challenges to processing, analysis, and storage of captured video, and prompts a reexamination of traditional routines used to process data in neuroscience and now demand improvements in both our hardware and software applications for processing, analyzing, and storing captured video. This project demonstrates the ease with which a dependable and affordable wide-field fluorescence imaging system can be assembled and integrated with behavior control and monitoring system such as found in a typical neuroscience laboratory. An Open-source MATLAB toolbox is employed to efficiently analyze and visualize large imaging data sets in a manner that is both interactive and fully automated. This software package provides a library of image pre-processing routines optimized for batch-processing of continuous functional fluorescence video, and additionally automates a fast unsupervised ROI detection and signal extraction routine. Further, an extension of this toolbox that uses GPU programming to process streaming video, enabling the identification, segmentation and extraction of neural activity signals on-line is described in which specific algorithms improve signal specificity and image quality at the single cell level in a behaving animal. This project describes the strategic ingredients for transforming a large bulk flow of raw continuous video into proportionally informative images and knowledge.en_US
dc.language.isoen_US
dc.rightsAttribution-NoDerivatives 4.0 Internationalen_US
dc.rights.urihttp://creativecommons.org/licenses/by-nd/4.0/
dc.subjectBiomedical engineeringen_US
dc.subjectCalcium imagingen_US
dc.subjectImage processingen_US
dc.subjectOptical imagingen_US
dc.titleTools for interfacing, extracting, and analyzing neural signals using wide-field fluorescence imaging and optogenetics in awake behaving miceen_US
dc.typeThesis/Dissertationen_US
dc.date.updated2019-08-09T16:04:18Z
etd.degree.nameDoctor of Philosophyen_US
etd.degree.leveldoctoralen_US
etd.degree.disciplineBiomedical Engineeringen_US
etd.degree.grantorBoston Universityen_US


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Attribution-NoDerivatives 4.0 International
Except where otherwise noted, this item's license is described as Attribution-NoDerivatives 4.0 International