Models that contain the Model Concept : Coincidence Detection

(The ability to distinguish whether or not events (typically action potentials which represent some feature of the external world) occur simultaneously or at different times.)
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    Models   Description
1.  A model for interaural time difference sensitivity in the medial superior olive (Zhou et al 2005)
This model simulates responses of neurons to interaural time difference (ITD) in the medial superior olive (MSO) of the mammalian brainstem. The model has a bipolar cell structure and incorporates two anatomic observations in the MSO: (1) the axon arises from the dendrite that receives ipsilateral inputs and (2) inhibitory synapses are located primarily on the soma in adult animals. Fine adjustment of the best ITD is achieved by the interplay of somatic sodium currents and synaptic inhibitory currents. The model suggests a mechanism for dynamically "fine-tuning" the ITD sensitivity of MSO cells by the opponency between depolarizing sodium currents and hyperpolarizing inhibitory currents.
2.  CA1 pyramidal neuron: conditional boosting of dendritic APs (Watanabe et al 2002)
Model files from the paper Watanabe S, Hoffman DA, Migliore M, Johnston D (2002). The experimental and modeling results support the hypothesis that dendritic K-A channels and the boosting of back-propagating action potentials contribute to the induction of LTP in CA1 neurons. See the paper for details. Questions about the model may be addressed to Michele Migliore: michele.migliore@pa.ibf.cnr.it
3.  CA1 pyramidal neuron: dendritic spike initiation (Gasparini et al 2004)
NEURON mod files from the paper: Sonia Gasparini, Michele Migliore, and Jeffrey C. Magee On the initiation and propagation of dendritic spikes in CA1 pyramidal neurons, J. Neurosci., J. Neurosci. 24:11046-11056 (2004).
4.  CA1 pyramidal neuron: integration of subthreshold inputs from PP and SC (Migliore 2003)
The model shows how the experimentally observed increase in the dendritic density of Ih and IA could have a major role in constraining the temporal integration window for the main CA1 synaptic inputs.
5.  CA1 pyramidal neuron: schizophrenic behavior (Migliore et al. 2011)
NEURON files from the paper: A modeling study suggesting how a reduction in the context-dependent input on CA1 pyramidal neurons could generate schizophrenic behavior. by M. Migliore, I. De Blasi, D. Tegolo, R. Migliore, Neural Networks,(2011), doi:10.1016/j.neunet.2011.01.001. Starting from the experimentally supported assumption on hippocampal neurons we explore an experimentally testable prediction at the single neuron level. The model shows how and to what extent a pathological hypofunction of a contextdependent distal input on a CA1 neuron can generate hallucinations by altering the normal recall of objects on which the neuron has been previously tuned. The results suggest that a change in the context during the recall phase may cause an occasional but very significant change in the set of active dendrites used for features recognition, leading to a distorted perception of objects.
6.  CA1 pyramidal neurons: binding properties and the magical number 7 (Migliore et al. 2008)
NEURON files from the paper: Single neuron binding properties and the magical number 7, by M. Migliore, G. Novara, D. Tegolo, Hippocampus, in press (2008). In an extensive series of simulations with realistic morphologies and active properties, we demonstrate how n radial (oblique) dendrites of these neurons may be used to bind n inputs to generate an output signal. The results suggest a possible neural code as the most effective n-ple of dendrites that can be used for short-term memory recollection of persons, objects, or places. Our analysis predicts a straightforward physiological explanation for the observed puzzling limit of about 7 short-term memory items that can be stored by humans.
7.  Coincidence detection in avian brainstem (Simon et al 1999)
A detailed biophysical model of coincidence detector neurons in the nucleus laminaris (auditory brainstem) which are purported to detect interaural time differences (ITDs) from Simon et al 1999.
8.  Coincident signals in Olfactory Bulb Granule Cell spines (Aghvami et al 2019)
"In the mammalian olfactory bulb, the inhibitory axonless granule cells (GCs) feature reciprocal synapses that interconnect them with the principal neurons of the bulb, mitral, and tufted cells. These synapses are located within large excitable spines that can generate local action potentials (APs) upon synaptic input (“spine spike”). Moreover, GCs can fire global APs that propagate throughout the dendrite. Strikingly, local postsynaptic Ca2+ entry summates mostly linearly with Ca2+ entry due to coincident global APs generated by glomerular stimulation, although some underlying conductances should be inactivated. We investigated this phenomenon by constructing a compartmental GC model to simulate the pairing of local and global signals as a function of their temporal separation ?t. These simulations yield strongly sublinear summation of spine Ca2+ entry for the case of perfect coincidence ?t = 0 ms. ..."
9.  Duration-tuned neurons from the inferior colliculus of the big brown bat (Aubie et al. 2009)
dtnet is a generalized neural network simulator written in C++ with an easy to use XML description language to generate arbitrary neural networks and then run simulations covering many different parameter values. For example, you can specify ranges of parameter values for several different connection weights and then automatically run simulations over all possible parameters. Graphing ability is built in as long as the free, open-source, graphing application GLE (http://glx.sourceforge.net/) is installed. Included in the examples folder are simulation descriptions that were used to generate the results in Aubie et al. (2009). Refer to the README file for instructions on compiling and running these examples. The most recent source code can be obtained from GitHub: <a href="https://github.com/baubie/dtnet">https://github.com/baubie/dtnet</a>
10.  Duration-tuned neurons from the inferior colliculus of vertebrates (Aubie et al. 2012)
These models reproduce the responses of duration-tuned neurons in the auditory midbrain of the big brown bat, the rat, the mouse and the frog (Aubie et al. 2012). They are written in the Python interface to NEURON and a subset of the figures from Aubie et al. (2012) are pre-set in run.py (raw data is generated and a separate graphing program must be used to visualize the results).
11.  Endocannabinoid dynamics gate spike-timing dependent depression and potentiation (Cui et al 2016)
The endocannabinoid (eCB) system is considered involved in synaptic depression. Recent reports have also linked eCBs to synaptic potentiation. However it is not known how eCB signaling may support such bidirectionality. To question the mechanisms of this phenomena in spike-timing dependent plasticity (STDP) at corticostriatal synapses, we combined electrophysiology experiments with biophysical modeling. We demonstrate that STDP is controlled by eCB levels and dynamics: prolonged and moderate levels of eCB lead to eCB-mediated long-term depression (eCB-tLTD) while short and large eCB transients produce eCB-mediated long-term potentiation (eCB-tLTP). Therefore, just like neurotransmitters glutamate or GABA, eCB form a bidirectional system.
12.  Ephaptic coupling in passive cable and MSO neuron models (Goldwyn & Rinzel 2016)
Simulation code to explore how the synchronous activity of a bundle of neurons generates extracellular voltage, and how this extracellular voltage influences the membrane potential of "nearby" neurons. A non-synaptic mechanism known as ephaptic coupling. A model of a passive cable population (including user-friendly matlab GUI) and a model of medial superior olive neurons are included.
13.  Function and energy constrain neuronal biophysics in coincidence detection (Remme et al 2018)
" ... We use models of conductance-based neurons constrained by experimentally observed characteristics with parameters varied within a physiologically realistic range. Our study shows that neuronal design of MSO cells does not compromise on function, but favors energetically less costly cell properties where possible without interfering with function."
14.  Globus pallidus neuron models with differing dendritic Na channel expression (Edgerton et al., 2010)
A set of 9 multi-compartmental rat GP neuron models (585 compartments) differing only in their expression of dendritic fast sodium channels were compared in their synaptic integration properties. Dendritic fast sodium channels were found to increase the importance of distal synapses (both excitatory AND inhibitory), increase spike timing variability with in vivo-like synaptic input, and make the model neurons highly sensitive to clustered synchronous excitation.
15.  Hopfield and Brody model (Hopfield, Brody 2000)
NEURON implementation of the Hopfield and Brody model from the papers: JJ Hopfield and CD Brody (2000) JJ Hopfield and CD Brody (2001). Instructions are provided in the below readme.txt file.
16.  Hopfield and Brody model (Hopfield, Brody 2000) (NEURON+python)
Demonstration of Hopfield-Brody snychronization using artificial cells in NEURON+python.
17.  IA and IT interact to set first spike latency (Molineux et al 2005)
Using patch clamp and modeling, we illustrate that spike latency characteristics are the product of an interplay between I(A) and low-threshold calcium current (I(T)) that requires a steady-state difference in the inactivation parameters of the currents. Furthermore, we show that the unique first-spike latency characteristics of stellate cells have important implications for the integration of coincident IPSPs and EPSPs, such that inhibition can shift first-spike latency to differentially modulate the probability of firing.
18.  Ih levels roles in bursting and regular-spiking subiculum pyramidal neurons (van Welie et al 2006)
Pyramidal neurons in the subiculum typically display either bursting or regular-spiking behavior. ... Here we report that bursting neurons posses a hyperpolarization-activated cation current (Ih) that is two-fold larger (conductance: 5.3 ± 0.5 nS) than in regularspiking neurons (2.2 ± 0.6 nS), while Ih exhibits similar voltage-dependent and kinetic properties in both classes of neurons. Bursting and regular-spiking neurons display similar morphology. The difference in Ih between the two classes is not responsible for the distinct firing patterns, since neither pharmacological blockade of Ih nor enhancement of Ih using a dynamic clamp affects the qualitative firing patterns. Instead, the difference in Ih between bursting and regular-spiking neurons determines the temporal integration of evoked synaptic input from the CA1 area. In response to 50 Hz stimulation, bursting neurons, with a large Ih, show ~50% less temporal summation than regular-spiking neurons. ... A computer simulation model of a subicular neuron with the properties of either a bursting or a regular-spiking neuron confirmed the pivotal role of Ih in temporal integration of synaptic input. These data suggest that in the subicular network, bursting neurons are better suited to discriminate the content of high frequency input, such as that occurring during gamma oscillations, compared to regular-spiking neurons. See paper for more and details.
19.  Integrate and fire model code for spike-based coincidence-detection (Heinz et al. 2001, others)
Model code relevant to three papers; two on level discrimination and one on masked detection at low frequencies.
20.  Microsaccades and synchrony coding in the retina (Masquelier et al. 2016)
We show that microsaccades (MS) enable efficient synchrony-based coding among the primate retinal ganglion cells (RGC). We find that each MS causes certain RGCs to fire synchronously, namely those whose receptive fields contain contrast edges after the MS. The emitted synchronous spike volley thus rapidly transmits the most salient edges of the stimulus. We demonstrate that the readout could be done rapidly by simple coincidence-detector neurons, and that the required connectivity could emerge spontaneously with spike timing-dependent plasticity.
21.  Modulation of temporal integration window (Migliore, Shepherd 2002)
Model simulation file from the paper M.Migliore and Gordon M. Shepherd Emerging rules for distributions of active dendritic properties underlying specific neuronal functions. Nature Rev. Neurosci. 3, 362-370 (2002).
22.  Optimal Localist and Distributed Coding Through STDP (Masquelier & Kheradpisheh 2018)
We show how a LIF neuron equipped with STDP can become optimally selective, in an unsupervised manner, to one or several repeating spike patterns, even when those patterns are hidden in Poisson spike trains.
23.  Optimal spatiotemporal spike pattern detection by STDP (Masquelier 2017)
We simulate a LIF neuron equipped with STDP. A pattern repeats in its inputs. The LIF progressively becomes selective to the repeating pattern, in an optimal manner.
24.  Oscillations, phase-of-firing coding and STDP: an efficient learning scheme (Masquelier et al. 2009)
The model demonstrates how a common oscillatory drive for a group of neurons formats and reliabilizes their spike times - through an activation-to-phase conversion - so that repeating activation patterns can be easily detected and learned by a downstream neuron equipped with STDP, and then recognized in just one oscillation cycle.
25.  Predicting formant-frequency discrimination in noise (Tan and Carney 2006)
"To better understand how the auditory system extracts speech signals in the presence of noise, discrimination thresholds for the second formant frequency were predicted with simulations of auditory-nerve responses. These predictions employed either average-rate information or combined rate and timing information, and either populations of model fibers tuned across a wide range of frequencies or a subset of fibers tuned to a restricted frequency range. In general, combined temporal and rate information for a small population of model fibers tuned near the formant frequency was most successful in replicating the trends reported in behavioral data for formant-frequency discrimination. ..."
26.  Pyramidal neuron coincidence detection tuned by dendritic branching pattern (Schaefer et al 2003)
"... We examined the relationship between dendritic arborization and the coupling between somatic and dendritic action potential (AP) initiation sites in layer 5 (L5) neocortical pyramidal neurons. Coupling was defined as the relative reduction in threshold for initiation of a dendritic calcium AP due to a coincident back-propagating AP. Simulations based on reconstructions of biocytin-filled cells showed that addition of oblique branches of the main apical dendrite in close proximity to the soma (d < 140 um) increases the coupling between the apical and axosomatic AP initiation zones, whereas incorporation of distal branches decreases coupling. ... We conclude that variation in dendritic arborization may be a key determinant of variability in coupling (49+-17%; range 19-83%; n = 37) and is likely to outweigh the contribution made by variations in active membrane properties. Thus coincidence detection of inputs arriving from different cortical layers is strongly regulated by differences in dendritic arborization."
27.  Relative spike time coding and STDP-based orientation selectivity in V1 (Masquelier 2012)
Phenomenological spiking model of the cat early visual system. We show how natural vision can drive spike time correlations on sufficiently fast time scales to lead to the acquisition of orientation-selective V1 neurons through STDP. This is possible without reference times such as stimulus onsets, or saccade landing times. But even when such reference times are available, we demonstrate that the relative spike times encode the images more robustly than the absolute ones.
28.  Salamander retinal ganglian cells: morphology influences firing (Sheasby, Fohlmeister 1999)
Nerve impulse entrainment and other excitation and passive phenomena are analyzed for a morphologically diverse and exhaustive data set (n=57) of realistic (3-dimensional computer traced) soma-dendritic tree structures of ganglion cells in the tiger salamander (Ambystoma tigrinum) retina.
29.  Schiz.-linked gene effects on intrinsic single-neuron excitability (Maki-Marttunen et al. 2016)
Python scripts for running NEURON simulations that model a layer V pyramidal cell with certain genetic variants implemented. The genes included are obtained from genome-wide association studies of schizophrenia.
30.  Spike timing detection in different forms of LTD (Doi et al 2005)
To understand the spike-timing detection mechanisms in cerebellar long-term depression (LTD), we developed a kinetic model of Ca dynamics within a Purkinje dendritic spine. In our kinetic simulation, IP3 was first produced via the metabotropic pathway of parallel fiber (PF) inputs, and the Ca influx in response to the climbing fiber (CF) input triggered regenerative Ca-induced Ca release from the internal stores via the IP3 receptors activated by the increased IP3. The delay in IP3 increase caused by the PF metabotropic pathway generated the optimal PF–CF interval. The Ca dynamics revealed a threshold for large Ca2 release that decreased as IP3 increased, and it coherently explained the different forms of LTD. See paper for more and details.
31.  Spike-Timing-Based Computation in Sound Localization (Goodman and Brette 2010)
" ... In neuron models consisting of spectro-temporal filtering and spiking nonlinearity, we found that the binaural structure induced by spatialized sounds is mapped to synchrony patterns that depend on source location rather than on source signal. Location-specific synchrony patterns would then result in the activation of location-specific assemblies of postsynaptic neurons. We designed a spiking neuron model which exploited this principle to locate a variety of sound sources in a virtual acoustic environment using measured human head-related transfer functions. ..."
32.  STDP allows fast rate-modulated coding with Poisson-like spike trains (Gilson et al. 2011)
The model demonstrates that a neuron equipped with STDP robustly detects repeating rate patterns among its afferents, from which the spikes are generated on the fly using inhomogenous Poisson sampling, provided those rates have narrow temporal peaks (10-20ms) - a condition met by many experimental Post-Stimulus Time Histograms (PSTH).
33.  Synaptic integration in a model of granule cells (Gabbiani et al 1994)
We have developed a compartmental model of a turtle cerebellar granule cell consisting of 13 compartments that represent the soma and 4 dendrites. We used this model to investigate the synaptic integration of mossy fiber inputs in granule cells. See reference or abstract at PubMed link below for more information.

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