Abstract:
:With the advancement in computer technology, it has become possible to fit complex models to neuronal data. In this work, we test how two methods can estimate parameters of simple neuron models (passive soma) to more complex ones (neuron with one dendritic cylinder and two active conductances). The first method uses classical voltage traces resulting from current pulses injection (time domain), while the second uses measures of the neuron's response to sinusoidal stimuli (frequency domain). Both methods estimate correctly the parameters in all cases studied. However, the time-domain method is slower and more prone to estimation errors in the cable parameters than the frequency-domain method. Because with noisy data the goodness of fit does not distinguish between different solutions, we suggest that running the estimation procedure a large number of times might help find a good solution and can provide information about the interactions between parameters. Also, because the formulation used for the model's response in the frequency domain is analytical, one can derive a local sensitivity analysis for each parameter. This analysis indicates how well a parameter is likely to be estimated and helps choose an optimal stimulation protocol. Finally, the tests suggest a strategy for fitting single-cell models using the two methods examined.
journal_name
J Comput Neuroscijournal_title
Journal of computational neuroscienceauthors
Tabak J,Murphey CR,Moore LEdoi
10.1023/a:1026531603628subject
Has Abstractpub_date
2000-11-01 00:00:00pages
215-36issue
3eissn
0929-5313issn
1573-6873journal_volume
9pub_type
杂志文章abstract::Implementation of double cable models to simulate the behavior of myelinated peripheral nerve fibers requires defining a segmentation of the internode between successive nodes of Ranvier. The number of internodal segments is a model parameter that is not well agreed on, with values in the literature ranging from 1 to ...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-014-0503-y
更新日期:2014-10-01 00:00:00
abstract::We have presented a new generation mechanism of slow spiking or repetitive discharges with extraordinarily long inter-spike intervals using the modified Hodgkin-Huxley equations (Doi and Kumagai, 2001). This generation process of slow firing is completely different from that of the well-known potassium A-current in th...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-005-2895-1
更新日期:2005-12-01 00:00:00
abstract::Within the theory that describes the hippocampus as a device for the on-line storage of complex memories, the crucial autoassociative operations are ascribed mainly to the recurrent CA3 network. The CA3-to-CA1 connections may still be important, both in completing information retrieval and in re-expanding, with minima...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/BF00961437
更新日期:1995-09-01 00:00:00
abstract::Nonlinear dynamics provides a complementary framework to control theory for the quantitative analysis of the oculomotor control system. This paper presents a number of findings relating to the aetiology and mechanics of the pathological ocular oscillation jerk congenital nystagmus (jerk CN). A range of time series ana...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-006-7816-4
更新日期:2006-10-01 00:00:00
abstract::The existence of electrical communication among pyramidal cells (PCs) in the adult cortex has been debated by neuroscientists for several decades. Gap junctions (GJs) among cortical interneurons have been well documented experimentally and their functional roles have been proposed by both computational neuroscientists...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-020-00762-5
更新日期:2020-11-01 00:00:00
abstract::The kinematics of the hand and fingers were studied during various keystrokes in typing. These movements were defined by 17 degrees of freedom of motion, and methods were developed to identify simplifying strategies in the execution of the task. Most of the analysis was restricted to the 11 degrees of freedom of the f...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/a:1008812426305
更新日期:1997-01-01 00:00:00
abstract::Gamma oscillations can synchronize with near zero phase lag over multiple cortical regions and between hemispheres, and between two distal sites in hippocampal slices. How synchronization can take place over long distances in a stable manner is considered an open question. The phase resetting curve (PRC) keeps track o...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-011-0315-2
更新日期:2011-10-01 00:00:00
abstract::During neural development sensory stimulation induces long-term changes in the receptive field of the neurons that encode the stimuli. The Bienenstock-Cooper-Munro (BCM) model was introduced to model and analyze this process computationally, and it remains one of the major models of unsupervised plasticity to this day...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-019-00715-7
更新日期:2019-04-01 00:00:00
abstract::Avian brain area HVC is known to be important for the production of birdsong. In zebra finches, each RA-projecting neuron in HVC emits a single burst of spikes during a song motif. The population of neurons is activated in a precisely timed, stereotyped sequence. We propose a model of these burst sequences that relies...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-007-0032-z
更新日期:2007-12-01 00:00:00
abstract::A Web-based simulation system of the spinal cord circuitry responsible for muscle control is described. The simulator employs two-compartment motoneuron models for S, FR and FF types, with synaptic inputs acting through conductance variations. Four motoneuron pools with their associated interneurons are represented in...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-008-0092-8
更新日期:2008-12-01 00:00:00
abstract::The goal of this paper is to design experiments that confirm the evidence of cognitive responses in functional near infrared spectroscopy and to establish relevant spectral subbands. Hemodynamic responses of brain during single-event trials in an odd-ball experiment are measured by functional near infrared spectroscop...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-005-5478-2
更新日期:2005-01-01 00:00:00
abstract::We study the dynamics and bifurcations of noise-free neurons coupled by gap junctions and inhibitory synapses, using both delayed delta functions and alpha functions to model the latter. We focus on the case of two cells, as in the studies of Chow and Kopell (2000) and Lewis and Rinzel (2003), but also show that stabl...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-006-9676-3
更新日期:2007-02-01 00:00:00
abstract::Replicability and reproducibility of computational models has been somewhat understudied by "the replication movement." In this paper, we draw on methodological studies into the replicability of psychological experiments and on the mechanistic account of explanation to analyze the functions of model replications and m...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-018-0702-z
更新日期:2018-12-01 00:00:00
abstract::In inactive stick insects, sensory information from the femoral chordotonal organ (fCO) about position and movement of the femur-tibia joint is transferred via local nonspiking interneurons onto extensor and flexor tibiae motoneurons. Information is processed by the interaction of antagonistic parallel pathways at two...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/BF00161131
更新日期:1996-09-01 00:00:00
abstract::When two-frame apparent motion stimuli are presented with an appropriate inter-stimulus interval (ISI), motion is perceived in the direction opposite to the actual image shift. Herein, we measured a simple eye movement, ocular following responses (OFRs), in macaque monkeys to examine the ISI reversal effect on oculomo...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-020-00756-3
更新日期:2020-07-17 00:00:00
abstract::Simultaneous recordings of spike trains from multiple single neurons are becoming commonplace. Understanding the interaction patterns among these spike trains remains a key research area. A question of interest is the evaluation of information flow between neurons through the analysis of whether one spike train exerts...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-008-0126-2
更新日期:2009-08-01 00:00:00
abstract::Activation of calcium/calmodulin-dependent protein kinase II (CaMKII) by calmodulin following calcium entry into the cell is important for long-term potentiation (LTP). Here a model of calmodulin binding and trapping by CaMKII in a dendritic spine was used to estimate levels and durations of CaMKII activation followin...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/a:1008969032563
更新日期:2000-01-01 00:00:00
abstract::The influence of unreliable synapses on the dynamic properties of a neural network is investigated for a homogeneous integrate-and-fire network with delayed inhibitory synapses. Numerical and analytical calculations show that the network relaxes to a state with dynamic clusters of identical size which permanently exch...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-008-0127-1
更新日期:2009-08-01 00:00:00
abstract::Neural mass models are successful in modeling brain rhythms as observed in macroscopic measurements such as the electroencephalogram (EEG). While the synaptic current is explicitly modeled in current models, the single cell electrophysiology is not taken into account. To allow for investigations of the effects of chan...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-014-0517-5
更新日期:2014-12-01 00:00:00
abstract::A neuron receives input from other neurons via electrical pulses, so-called spikes. The pulse-like nature of the input is frequently neglected in analytical studies; instead, the input is usually approximated to be Gaussian. Recent experimental studies have shown, however, that an assumption underlying this approximat...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-017-0649-5
更新日期:2017-08-01 00:00:00
abstract::Many neuron types exhibit preferred frequency responses in their voltage amplitude (resonance) or phase shift to subthreshold oscillatory currents, but the effect of biophysical parameters on these properties is not well understood. We propose a general framework to analyze the role of different ionic currents and the...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-013-0483-3
更新日期:2014-08-01 00:00:00
abstract::Following a flashed stimulus, I show that a simple neurophysiological mechanism in the primary visual system can generate orientation selectivity based on the first incoming spikes. A biological model of the lateral geniculate nucleus generates an asynchronous wave of spikes, with the most strongly activated neurons f...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/a:1027420012134
更新日期:2003-11-01 00:00:00
abstract::We developed a multicompartmental Hodgkin-Huxley model of the Hermissenda type-B photoreceptor and used it to address the relative contributions of reductions of two K+ currents, IA and IC, to changes in cellular excitability and synaptic strength that occur in these cells after associative learning. We found that red...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/BF00160809
更新日期:1996-06-01 00:00:00
abstract::The timing of transmitter release from nerve endings is considered nowadays as one of the factors determining the plasticity and efficacy of synaptic transmission. In the neuromuscular junction, the moments of release of individual acetylcholine quanta are related to the synaptic delays of uniquantal endplate currents...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-015-0567-3
更新日期:2015-10-01 00:00:00
abstract::The precise mapping of how complex patterns of synaptic inputs are integrated into specific patterns of spiking output is an essential step in the characterization of the cellular basis of network dynamics and function. Relative to other principal neurons of the hippocampus, the electrophysiology of CA1 pyramidal cell...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-006-8797-z
更新日期:2006-10-01 00:00:00
abstract::We present a new method to characterize multi-input and output neuronal systems using information theory. To obtain a lower bound of transinformation we take three steps: (1) Estimation of the deterministic response to isolate components carrying stimulus information. The deviation of the original response from the de...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/a:1016583328930
更新日期:2002-05-01 00:00:00
abstract::The response of neurons to external stimuli greatly depends on the intrinsic dynamics of the network. Here, the intrinsic dynamics are modeled as coupling and the external input is modeled as shared and unshared noise. We assume the neurons are repetitively firing action potentials (i.e., neural oscillators), are weak...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-008-0120-8
更新日期:2009-06-01 00:00:00
abstract::Mathematical neuronal models are normally expressed using differential equations. The Parker-Sochacki method is a new technique for the numerical integration of differential equations applicable to many neuronal models. Using this method, the solution order can be adapted according to the local conditions at each time...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-008-0131-5
更新日期:2009-08-01 00:00:00
abstract::Firing-rate models provide a practical tool for studying signal processing in the early visual system, permitting more thorough mathematical analysis than spike-based models. We show here that essential response properties of relay cells in the lateral geniculate nucleus (LGN) can be captured by surprisingly simple fi...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-013-0456-6
更新日期:2013-12-01 00:00:00
abstract::Information maximization has long been suggested as the underlying coding strategy of the primary visual cortex (V1). Grouping image sequences into blocks has been shown by others to improve agreement between experiments and theory. We have studied the effect of temporal convolution on the formation of spatiotemporal ...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/a:1013723131070
更新日期:2001-11-01 00:00:00