Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON

Mattioni, Michele; Cohen, Uri; Novère, Nicolas Le

doi:10.3389/fninf.2012.00020

Cited by 9 publications

(5 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“… (A) The detailed reconstruction of the mitral cells used for the model. Functional compartments are color coded [ 61 ]. (B) The simplified geometry of the mitral cell, where the functional compartments were reduced to cylindrical sections while preserving their membrane surface area and passive properties.…”

Section: Supporting Informationmentioning

confidence: 99%

Prolonged Intracellular Na+ Dynamics Govern Electrical Activity in Accessory Olfactory Bulb Mitral Cells

Zylbertal¹,

Kahan

Ben‐Shaul

et al. 2015

PLoS Biol

View full text Add to dashboard Cite

Persistent activity has been reported in many brain areas and is hypothesized to mediate working memory and emotional brain states and to rely upon network or biophysical feedback. Here, we demonstrate a novel mechanism by which persistent neuronal activity can be generated without feedback, relying instead on the slow removal of Na+ from neurons following bursts of activity. We show that mitral cells in the accessory olfactory bulb (AOB), which plays a major role in mammalian social behavior, may respond to a brief sensory stimulation with persistent firing. By combining electrical recordings, Ca2+ and Na+ imaging, and realistic computational modeling, we explored the mechanisms underlying the persistent activity in AOB mitral cells. We found that the exceptionally slow inward current that underlies this activity is governed by prolonged dynamics of intracellular Na+ ([Na+]i), which affects neuronal electrical activity via several pathways. Specifically, elevated dendritic [Na+]i reverses the Na+-Ca2+ exchanger activity, thus modifying the [Ca2+]i set-point. This process, which relies on ubiquitous membrane mechanisms, is likely to play a role in other neuronal types in various brain regions.

show abstract

Section: Supporting Informationmentioning

confidence: 99%

Prolonged Intracellular Na+ Dynamics Govern Electrical Activity in Accessory Olfactory Bulb Mitral Cells

Zylbertal¹,

Kahan

Ben‐Shaul

et al. 2015

PLoS Biol

View full text Add to dashboard Cite

show abstract

“…There are other simulation management resources available, some of which have overlapping functionality with SimTracker, including NeuroConstruct (Gleeson et al, 2007), Net-PyNE (http://www.neurosimlab.org/netpyne/), Lancet (Stevens et al, 2013), NeuroTools (https://github.com/NeuralEnsemble/NeuroTools), NeuronVisio (Mattioni et al, 2012), and Sumatra (Davison, 2012). However, a combination of properties renders SimTracker unique and a necessary addition to the other available tools.…”

mentioning

confidence: 99%

SimTracker tool and code template to design, manage and analyze neural network model simulations in parallel NEURON

Bezaire

Raikov

Burk

et al. 2016

Preprint

View full text Add to dashboard Cite

Advances in technical computing enable larger and more detailed neural models that can incorporate ever more of the rapidly expanding body of quantitative neuroscience data. In principle, such complex network models that are strongly constrained by experimental data could direct experimental research and provide novel insights into experimental observations. However, as network models grow in complexity and scale, the necessary tasks of development and organization become unwieldy. Further, the models risk becoming inaccessible to experimentalists and other modelers, and their results may then be seen as less relevant to experimental work. To address these obstacles, we developed a tool for managing simulations called SimTracker. It supports users at each step of the modeling process, including execution of large scale parallel models on supercomputers. SimTracker is suitable for users with a range of modeling experience. SimTracker can be a valuable modeling resource that promotes iterative progress between experiment and model.

show abstract

“…The program runs on Windows, Mac, Linux, and on parallel architectures including Beowulf clusters, IBM Blue Gene, and Cray XT3. The popularity of NEURON also encouraged the implementation of ancillary tools such as Neuronvisio, an enhanced interface allowing interactive 3D model representations and saving/reloading of simulation results (Mattioni et al, 2012; michelemattioni.me/neuronvisio). …”

Section: Tools and Resources For Digital Reconstructionsmentioning

confidence: 99%

Neuronal Morphology Goes Digital: A Research Hub for Cellular and System Neuroscience

Parekh

Ascoli

2013

Neuron

182

133

View full text Add to dashboard Cite

Summary The importance of neuronal morphology in brain function has been recognized for over a century. The broad applicability of “digital reconstructions” of neuron morphology across neuroscience sub-disciplines has stimulated the rapid development of numerous synergistic tools for data acquisition, anatomical analysis, three-dimensional rendering, electrophysiological simulation, growth models, and data sharing. Here we discuss the processes of histological labeling, microscopic imaging, and semi-automated tracing. Moreover, we provide an annotated compilation of currently available resources in this rich research “ecosystem” as a central reference for experimental and computational neuroscience.

show abstract

Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON

Cited by 9 publications

References 22 publications

Prolonged Intracellular Na+ Dynamics Govern Electrical Activity in Accessory Olfactory Bulb Mitral Cells

Prolonged Intracellular Na+ Dynamics Govern Electrical Activity in Accessory Olfactory Bulb Mitral Cells

SimTracker tool and code template to design, manage and analyze neural network model simulations in parallel NEURON

Neuronal Morphology Goes Digital: A Research Hub for Cellular and System Neuroscience

Contact Info

Product

Resources

About