scholarly journals Video rate volumetric Ca2+ imaging across cortical layers using Seeded Iterative Demixing (SID) microscopy

2017 ◽  
Author(s):  
Tobias Nöbauer ◽  
Oliver Skocek ◽  
Alejandro J. Pernía-Andrade ◽  
Lukas Weilguny ◽  
Francisca Martinez Traub ◽  
...  
Keyword(s):  
High Speed ◽  
Computational Cost ◽  
Neuronal Dynamics ◽  
Tissue Scattering ◽  
Mouse Cortex ◽  
New Applications ◽  
Source Extraction ◽  
Neuroscience Community ◽  
Wide Dissemination

Light-field microscopy (LFM) is a scalable approach for volumetric Ca2+ imaging with the highest volumetric acquisition rates (up to 100 Hz). While this has enabled high-speed whole-brain Ca2+ imaging in small semi-transparent specimen, tissue scattering has limited its application in the rodent brain. Here we introduce Seeded Iterative Demixing (SID), a computational source extraction technique that extends LFM to the scattering mammalian cortex. Using GCaMP-expressing mice we demonstrate SID’s ability to capture neuronal dynamics in vivo within a volume of 900×900×260μm located as deep as 380 μm in the mouse cortex and hippocampus at 30 Hz volume rate while faithfully discriminating signals from neurons as close as 20 μm, at three orders of magnitude reduced computational cost. The simplicity and scalability of LFM, coupled with the performance of SID opens up a range of new applications including closed-loop experiments and is expected to propel its wide dissemination within the neuroscience community.

scholarly journals Event-Driven Simulation Scheme for Spiking Neural Networks Using Lookup Tables to Characterize Neuronal Dynamics

2006 ◽  
Vol 18 (12) ◽  
pp. 2959-2993 ◽  
Author(s):  
Eduardo Ros ◽  
Richard Carrillo ◽  
Eva M. Ortigosa ◽  
Boris Barbour ◽  
Rodrigo Agís
Keyword(s):  
Synaptic Plasticity ◽  
High Speed ◽  
Large Scale ◽  
Computational Cost ◽  
Brain Structures ◽  
Spike Timing ◽  
Neuronal Dynamics ◽  
Event Driven ◽  
Synaptic Dynamics

Nearly all neuronal information processing and interneuronal communication in the brain involves action potentials, or spikes, which drive the short-term synaptic dynamics of neurons, but also their long-term dynamics, via synaptic plasticity. In many brain structures, action potential activity is considered to be sparse. This sparseness of activity has been exploited to reduce the computational cost of large-scale network simulations, through the development of event-driven simulation schemes. However, existing event-driven simulations schemes use extremely simplified neuronal models. Here, we implement and evaluate critically an event-driven algorithm (ED-LUT) that uses precalculated look-up tables to characterize synaptic and neuronal dynamics. This approach enables the use of more complex (and realistic) neuronal models or data in representing the neurons, while retaining the advantage of high-speed simulation. We demonstrate the method's application for neurons containing exponential synaptic conductances, thereby implementing shunting inhibition, a phenomenon that is critical to cellular computation. We also introduce an improved two-stage event-queue algorithm, which allows the simulations to scale efficiently to highly connected networks with arbitrary propagation delays. Finally, the scheme readily accommodates implementation of synaptic plasticity mechanisms that depend on spike timing, enabling future simulations to explore issues of long-term learning and adaptation in large-scale networks.

Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach

2018 ◽  
Author(s):  
Benjamin R. Jagger ◽  
Christoper T. Lee ◽  
Rommie Amaro
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Small Molecule ◽  
Brownian Dynamics ◽  
Model Simulation ◽  
Computational Cost ◽  
Lead Selection ◽  
Delta G ◽  
Dynamics Simulations

<p>The ranking of small molecule binders by their kinetic (kon and koff) and thermodynamic (delta G) properties can be a valuable metric for lead selection and optimization in a drug discovery campaign, as these quantities are often indicators of in vivo efficacy. Efficient and accurate predictions of these quantities can aid the in drug discovery effort, acting as a screening step. We have previously described a hybrid molecular dynamics, Brownian dynamics, and milestoning model, Simulation Enabled Estimation of Kinetic Rates (SEEKR), that can predict kon’s, koff’s, and G’s. Here we demonstrate the effectiveness of this approach for ranking a series of seven small molecule compounds for the model system, -cyclodextrin, based on predicted kon’s and koff’s. We compare our results using SEEKR to experimentally determined rates as well as rates calculated using long-timescale molecular dynamics simulations and show that SEEKR can effectively rank the compounds by koff and G with reduced computational cost. We also provide a discussion of convergence properties and sensitivities of calculations with SEEKR to establish “best practices” for its future use.</p>

scholarly journals High-speed volumetric two-photon fluorescence imaging of neurovascular dynamics

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jiang Lan Fan ◽  
Jose A. Rivera ◽  
Wei Sun ◽  
John Peterson ◽  
Henry Haeberle ◽  
...  
Keyword(s):  
Blood Flow ◽  
High Speed ◽  
Laser Scanning ◽  
Three Dimensional ◽  
Laser Scanning Microscopy ◽  
Fluorescence Signal ◽  
Imaging Method ◽  
Spatiotemporal Resolution ◽  
Two Photon

AbstractUnderstanding the structure and function of vasculature in the brain requires us to monitor distributed hemodynamics at high spatial and temporal resolution in three-dimensional (3D) volumes in vivo. Currently, a volumetric vasculature imaging method with sub-capillary spatial resolution and blood flow-resolving speed is lacking. Here, using two-photon laser scanning microscopy (TPLSM) with an axially extended Bessel focus, we capture volumetric hemodynamics in the awake mouse brain at a spatiotemporal resolution sufficient for measuring capillary size and blood flow. With Bessel TPLSM, the fluorescence signal of a vessel becomes proportional to its size, which enables convenient intensity-based analysis of vessel dilation and constriction dynamics in large volumes. We observe entrainment of vasodilation and vasoconstriction with pupil diameter and measure 3D blood flow at 99 volumes/second. Demonstrating high-throughput monitoring of hemodynamics in the awake brain, we expect Bessel TPLSM to make broad impacts on neurovasculature research.

scholarly journals High-speed high-resolution laser diode-based photoacoustic microscopy for in vivo microvasculature imaging

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xiufeng Li ◽  
Victor T C Tsang ◽  
Lei Kang ◽  
Yan Zhang ◽  
Terence T W Wong
Keyword(s):  
High Resolution ◽  
High Speed ◽  
High Performance ◽  
Continuous Wave ◽  
Signal To Noise Ratio ◽  
Cost Effective ◽  
High Signal ◽  
Photoacoustic Microscopy ◽  
Mouse Ear

AbstractLaser diodes (LDs) have been considered as cost-effective and compact excitation sources to overcome the requirement of costly and bulky pulsed laser sources that are commonly used in photoacoustic microscopy (PAM). However, the spatial resolution and/or imaging speed of previously reported LD-based PAM systems have not been optimized simultaneously. In this paper, we developed a high-speed and high-resolution LD-based PAM system using a continuous wave LD, operating at a pulsed mode, with a repetition rate of 30 kHz, as an excitation source. A hybrid scanning mechanism that synchronizes a one-dimensional galvanometer mirror and a two-dimensional motorized stage is applied to achieve a fast imaging capability without signal averaging due to the high signal-to-noise ratio. By optimizing the optical system, a high lateral resolution of 4.8 μm has been achieved. In vivo microvasculature imaging of a mouse ear has been demonstrated to show the high performance of our LD-based PAM system.

Using Wavelet Analysis to Distinguish Cavitation Acoustic Emissions From Blunt Impact Noise

2021 ◽  
Author(s):  
Christopher Eckersley ◽  
Joost Op 't Eynde ◽  
Mitchell Abrams ◽  
Cameron R. Bass
Keyword(s):  
Wavelet Transform ◽  
High Speed ◽  
Acoustic Noise ◽  
Bubble Formation ◽  
Acoustic Emissions ◽  
Wide Band ◽  
Water Tank ◽  
Impact Noise ◽  
Blunt Impact

Abstract Cavitation has been shown to have implications for head injury, but currently there is no solution for detecting the formation of cavitation through the skull during blunt impact. The goal of this communication is to confirm the wideband acoustic wavelet signature of cavitation collapse, and determine that this signature can be differentiated from the noise of a blunt impact. A controlled, laser induced cavitation study was conducted in an isolated water tank to confirm the wide band acoustic signature of cavitation collapse in the absence of a blunt impact. A clear acrylic surrogate head was impacted to induce blunt impact cavitation. The bubble formation was imaged using a high speed camera, and the collapse was synched up with the wavelet transform of the acoustic emission. Wideband acoustic response is seen in wavelet transform of positive laser induced cavitation tests, but absent in laser induced negative controls. Clear acrylic surrogate tests showed the wideband acoustic wavelet signature of collapse can be differentiated from acoustic noise generated by a blunt impact. Broadband acoustic signal can be used as a biomarker to detect the incidence of cavitation through the skull as it consists of frequencies that are low enough to potentially pass through the skull but high enough to differentiate from blunt impact noise. This lays the foundation for a vital tool to conduct CSF cavitation research in-vivo.

Numerical simulation of humidification and heating during inspiration within an adult nose

2012 ◽  
Vol 50 (2) ◽  
pp. 157-164
Author(s):  
F. Sommer ◽  
R. Kroger ◽  
J. Lindemann
Keyword(s):  
Numerical Simulations ◽  
High Speed ◽  
Middle Turbinate ◽  
Multislice Ct ◽  
Respiratory Cycle ◽  
In Vivo Measurements ◽  
Airflow Distribution ◽  
The Impact ◽  
Human Nose

Background: The temperature of inhaled air is highly relevant for the humidification process. Narrow anatomical conditions limit possibilities for in vivo measurements. Numerical simulations offer a great potential to examine the function of the human nose. Objective: In the present study, the nasal humidification of inhaled air was simulated simultaneously with temperature distribution during a respiratory cycle. Methods: A realistic nose model based on a multislice CT scan was created. The simulation was performed by the Software Fluent(r). Boundary conditions were based on previous in vivo measurements. Inhaled air had a temperature of 20(deg)C and relative humidity of 30%. The wall temperature was assumed to be variable from 34(deg)C to 30(deg)C with constant humidity saturation of 100% during the respiratory cycle. Results: A substantial increase in temperature and humidity can be observed after passing the nasal valve area. Areas with high speed air flow, e.g. the space around the turbinates, show an intensive humidification and heating potential. Inspired air reaches 95% humidity and 28(deg)C within the nasopharynx. Conclusion: The human nose features an enormous humidification and heating capability. Warming and humidification are dependent on each other and show a similar spacial pattern. Concerning the climatisation function, the middle turbinate is of high importance. In contrast to in vivo measurements, numerical simulations can explore the impact of airflow distribution on nasal air conditioning. They are an effective method to investigate nasal pathologies and impacts of surgical procedures.

In vivo imaging with high-speed full-range complex spectral domain optical coherence tomography

2005 ◽  
Author(s):  
Erich Goetzinger ◽  
Michael Pircher ◽  
Rainer A. Leitgeb ◽  
Adolf F. Fercher ◽  
Christoph K. Hitzenberger
Keyword(s):  
Optical Coherence Tomography ◽  
In Vivo Imaging ◽  
High Speed ◽  
Full Range ◽  
Spectral Domain ◽  
Optical Coherence
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