The roles of supervised machine learning in systems neuroscience

Progress in Neurobiology, Год журнала: 2019, Номер 175, С. 126 - 137

Опубликована: Фев. 9, 2019

Язык: Английский

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Deciphering the molecular mechanism responsible for GCaMP6m's Ca2+-dependent change in fluorescence

PLoS ONE, Год журнала: 2017, Номер 12(2), С. e0170934 - e0170934

Опубликована: Фев. 9, 2017

The goal of this work is to determine how GCaMP6m's fluorescence altered in response Ca2+-binding. Our detailed spectroscopic study reveals the simplest explanation for GCaMP6m changes Ca2+ with a four-state model, which Ca2+-dependent change chromophore protonation state, due shift pKa, predominant factor. pKa quantitatively explained by electrostatic potential around conformational that occur protein when calmodulin binds and interacts M13 peptide. absolute values Ca2+-free Ca2+-saturated states are critical its high signal-to-noise ratio. This mechanism has important implications further improvements potentially other similarly designed biosensors.

Язык: Английский

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An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics

PLoS Computational Biology, Год журнала: 2017, Номер 13(6), С. e1005526 - e1005526

Опубликована: Июнь 7, 2017

The development of new imaging and optogenetics techniques to study the dynamics large neuronal circuits is generating datasets unprecedented volume complexity, demanding appropriate analysis tools. We present a comprehensive computational workflow for population calcium dynamics. toolbox includes newly developed algorithms interactive tools image pre-processing segmentation, estimation significant single-neuron single-trial signals, mapping event-related responses, detection activity-correlated clusters, exploration dynamics, clusters' features against surrogate control datasets. modules are integrated in modular versatile processing pipeline, adaptable different needs. clustering module capable detecting flexible, dynamically activated assemblies, consistent with distributed coding brain. demonstrate suitability variety open-source code, step-by-step tutorial case dataset available at https://github.com/zebrain-lab/Toolbox-Romano-et-al.

Язык: Английский

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Computational processing of neural recordings from calcium imaging data

Current Opinion in Neurobiology, Год журнала: 2018, Номер 55, С. 22 - 31

Опубликована: Дек. 7, 2018

Electrophysiology has long been the workhorse of neuroscience, allowing scientists to record with millisecond precision action potentials generated by neurons in vivo. Recently, calcium imaging fluorescent indicators emerged as a powerful alternative. This technique its own strengths and weaknesses unique data processing problems interpretation confounds. Here we review computational methods that convert raw movies estimates single neuron spike times minimal human supervision. By computationally addressing imaging, these hold promise significantly improving quality. We also introduce new metric evaluate output pipelines, which is based on cluster isolation distance routinely used electrophysiology.

Язык: Английский

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Integrative whole-brain neuroscience in larval zebrafish

Current Opinion in Neurobiology, Год журнала: 2018, Номер 50, С. 136 - 145

Опубликована: Март 20, 2018

Язык: Английский

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