| | Models | Description |
| 1. |
5-neuron-model of neocortex for producing realistic extracellular AP shapes (Van Dijck et al. 2012)
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This is a 5-neuron model of neocortex, containing one tufted layer-5 pyramidal cell, two non-tufted pyramidal cells, and two inhibitory interneurons. It was used to reproduce extracellular spike shapes in a study comparing algorithms for spike sorting and electrode selection. The neuron models are adapted from Dyhrfjeld-Johnsen et al. (2005). |
| 2. |
A Layer V CCS type pyramidal cell, inhibitory synapse current conduction (Kubota Y et al., 2015)
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A layer V crossed-corticostriatal (CCS) ‘slender untufted’ pyramidal cell model of rat frontal cortex was built using Neurolucida tracing as well as 3D reconstructed dendrites of serial electron micrographs to give the model as authentic morphology as possible. |
| 3. |
A Model Circuit of Thalamocortical Convergence (Behuret et al. 2013)
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“…
Using dynamic-clamp techniques in thalamic slices in vitro, we combined theoretical and experimental
approaches to implement a realistic hybrid retino-thalamo-cortical pathway mixing biological cells and simulated circuits.
…
The study of
the impact of the simulated cortical input on the global retinocortical signal transfer efficiency revealed a novel control
mechanism resulting from the collective resonance of all thalamic relay neurons.
We show here that the transfer efficiency
of sensory input transmission depends on three key features: i) the number of thalamocortical cells involved in the many-to-one
convergence from thalamus to cortex, ii) the statistics of the corticothalamic synaptic bombardment and iii) the level of
correlation imposed between converging thalamic relay cells.
In particular, our results demonstrate counterintuitively that
the retinocortical signal transfer efficiency increases when the level of correlation across thalamic cells decreases.
…”
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| 4. |
A multilayer cortical model to study seizure propagation across microdomains (Basu et al. 2015)
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A realistic neural network was used to simulate a region of neocortex to obtain extracellular LFPs from ‘virtual micro-electrodes’ and produce test data for comparison with multisite microelectrode recordings. A model was implemented in the GENESIS neurosimulator. A simulated region of cortex was represented by layers 2/3, 5/6 (interneurons and pyramidal cells) and layer 4 stelate cells, spaced at 25 µm in each horizontal direction. Pyramidal cells received AMPA and NMDA inputs from neighboring cells at the basal and apical dendrites.
The LFP data was generated by simulating 16-site electrode array with the help of ‘efield’ objects arranged at the predetermined positions with respect to the surface of the simulated network. The LFP for the model is derived from a weighted average of the current sources summed over all cellular compartments. Cell models were taken from from Traub et al. (2005) J Neurophysiol 93(4):2194-232. |
| 5. |
A set of reduced models of layer 5 pyramidal neurons (Bahl et al. 2012)
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These are the NEURON files for 10 different models of a reduced L5 pyramidal neuron. The parameters were obtained by automatically fitting the models to experimental data using a multi objective evolutionary search strategy. Details on the algorithm can be found at
http://www.g-node.org/emoo and in Bahl et al. (2012).
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| 6. |
Accurate and fast simulation of channel noise in conductance-based model neurons (Linaro et al 2011)
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We introduce and operatively present a general method to simulate channel noise in conductance-based model neurons, with modest computational overheads.
Our approach may be considered as an accurate generalization of previous proposal methods,
to the case of voltage-, ion-, and ligand-gated channels with arbitrary complexity.
We focus on the discrete Markov process descriptions, routinely employed in experimental
identification of voltage-gated channels and synaptic receptors. |
| 7. |
Action Potential initiation and backpropagation in Neocortical L5 Pyramidal Neuron (Hu et al. 2009)
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"...Previous computational studies have yielded conflicting conclusions
about the role of Na+ channel density and biophysical properties in
action potential initiation as a result of inconsistent estimates of
channel density. Our modeling studies integrated the immunostaining
and electrophysiological results and showed that the lowest
threshold for action potential initiation at the distal AIS was largely
determined by the density of low-threshold Nav1.6 channels ... Distinct from the function of Nav1.6 channel, the Nav1.2 channel
may control action potential backpropagation because of its high
density at the proximal AIS and high threshold. ... In conclusion, distal AIS accumulation of Nav1.6 channels determines
the low threshold for action potential initiation; whereas
proximal AIS accumulation of Nav1.2 channels sets the threshold for
the generation of somatodendritic potentials and ensures action
potential backpropagation to the soma and dendrites. Thus, Nav1.6
and Nav1.2 channels serve distinct functions in action potential
initiation and backpropagation." |
| 8. |
Action potential-evoked Na+ influx similar in axon and soma (Fleidervish et al. 2010) (Python)
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"In cortical pyramidal neurons, the axon initial segment (AIS) is pivotal in synaptic integration. It has been asserted that this is because there is a high density of Na+ channels in the AIS. However, we found that action potential-associated Na+ flux, as measured by high-speed fluorescence Na+ imaging, was about threefold larger in the rat AIS than in the soma. Spike-evoked Na+ flux in the AIS and the first node of Ranvier was similar and was eightfold lower in basal dendrites. ... In computer simulations, these data were consistent with the known features of action potential generation in these neurons." |
| 9. |
Biologically Constrained Basal Ganglia model (BCBG model) (Lienard, Girard 2014)
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We studied the physiology and function of the basal ganglia through the design of mean-field models of the whole basal ganglia. The parameterizations are optimized with multi-objective evolutionary algorithm to respect best a collection of numerous anatomical data and electrophysiological data. The main outcomes of our study are: • The strength of the GPe to GPi/SNr connection does not support opposed activities in the GPe and GPi/SNr. • STN and MSN target more the GPe than the GPi/SNr. • Selection arises from the structure of the basal ganglia, without properly segregated direct and indirect pathways and without specific inputs from pyramidal tract neurons of the cortex. Selection is enhanced when the projection from GPe to GPi/SNr has a diffuse pattern. |
| 10. |
Calcium spikes in basal dendrites (Kampa and Stuart 2006)
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This model was published in Kampa & Stuart (2006) J Neurosci 26(28):7424-32. The simulation creates two plots showing voltage and calcium changes in basal dendrites of layer 5 pyramidal neurons during action potential backpropagation.
created by B. Kampa (2006) |
| 11. |
Combining modeling, deep learning for MEA neuron localization, classification (Buccino et al 2018)
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"Neural circuits typically consist of many different types of neurons, and one faces a challenge in disentangling their individual contributions in measured neural activity. Classification of cells into inhibitory and excitatory neurons and localization of neurons on the basis of extracellular recordings are frequently employed procedures. Current approaches, however, need a lot of human intervention, which makes them slow, biased, and unreliable. In light of recent advances in deep learning techniques and exploiting the availability of neuron models with quasi-realistic three-dimensional morphology and physiological properties, we present a framework for automatized and objective classification and localization of cells based on the spatiotemporal profiles of the extracellular action potentials recorded by multielectrode arrays. We train convolutional neural networks on simulated signals from a large set of cell models and show that our framework can predict the position of neurons with high accuracy, more precisely than current state-of-the-art methods. Our method is also able to classify whether a neuron is excitatory or inhibitory with very high accuracy, substantially improving on commonly used clustering techniques. ..." |
