scholarly journals Traditional waveform based spike sorting yields biased rate code estimates

2009 ◽  
Vol 106 (17) ◽  
pp. 6921-6926 ◽  
Author(s):  
Valérie Ventura
Keyword(s):  
Tuning Curve ◽  
Receptive Fields ◽  
Environmental Parameters ◽  
Spike Trains ◽  
Spike Sorting ◽  
Curve Estimation ◽  
Tuning Curves ◽  
Firing Rates ◽  
Neurophysiological Data ◽  
And Behavior

Much of neuroscience has to do with relating neural activity and behavior or environment. One common measure of this relationship is the firing rates of neurons as functions of behavioral or environmental parameters, often called tuning functions and receptive fields. Firing rates are estimated from the spike trains of neurons recorded by electrodes implanted in the brain. Individual neurons' spike trains are not typically readily available, because the signal collected at an electrode is often a mixture of activities from different neurons and noise. Extracting individual neurons' spike trains from voltage signals, which is known as spike sorting, is one of the most important data analysis problems in neuroscience, because it has to be undertaken prior to any analysis of neurophysiological data in which more than one neuron is believed to be recorded on a single electrode. All current spike-sorting methods consist of clustering the characteristic spike waveforms of neurons. The sequence of first spike sorting based on waveforms, then estimating tuning functions, has long been the accepted way to proceed. Here, we argue that the covariates that modulate tuning functions also contain information about spike identities, and that if tuning information is ignored for spike sorting, the resulting tuning function estimates are biased and inconsistent, unless spikes can be classified with perfect accuracy. This means, for example, that the commonly used peristimulus time histogram is a biased estimate of the firing rate of a neuron that is not perfectly isolated. We further argue that the correct conceptual way to view the problem out is to note that spike sorting provides information about rate estimation and vice versa, so that the two relationships should be considered simultaneously rather than sequentially. Indeed we show that when spike sorting and tuning-curve estimation are performed in parallel, unbiased estimates of tuning curves can be recovered even from imperfectly sorted neurons.

scholarly journals Response properties of single neurons in higher level auditory cortex of adult songbirds

2019 ◽  
Vol 121 (1) ◽  
pp. 218-237 ◽  
Author(s):  
Sarah W. Bottjer ◽  
Andrew A. Ronald ◽  
Tiara Kaye
Keyword(s):  
Auditory Cortex ◽  
Tuning Curve ◽  
Vocal Learning ◽  
Spiking Neurons ◽  
Complex Sounds ◽  
Response Properties ◽  
Tuning Curves ◽  
Firing Rates ◽  
Fast Spiking ◽  
High Firing

The caudomedial nidopallium (NCM) is a higher level region of auditory cortex in songbirds that has been implicated in encoding learned vocalizations and mediating perception of complex sounds. We made cell-attached recordings in awake adult male zebra finches ( Taeniopygia guttata) to characterize responses of single NCM neurons to playback of tones and songs. Neurons fell into two broad classes: narrow fast-spiking cells and broad sparsely firing cells. Virtually all narrow-spiking cells responded to playback of pure tones, compared with approximately half of broad-spiking cells. In addition, narrow-spiking cells tended to have lower thresholds and faster, less variable spike onset latencies than did broad-spiking cells, as well as higher firing rates. Tonal responses of narrow-spiking cells also showed broader ranges for both frequency and amplitude compared with broad-spiking neurons and were more apt to have V-shaped tuning curves compared with broad-spiking neurons, which tended to have complex (discontinuous), columnar, or O-shaped frequency response areas. In response to playback of conspecific songs, narrow-spiking neurons showed high firing rates and low levels of selectivity whereas broad-spiking neurons responded sparsely and selectively. Broad-spiking neurons in which tones failed to evoke a response showed greater song selectivity compared with those with a clear tuning curve. These results are consistent with the idea that narrow-spiking neurons represent putative fast-spiking interneurons, which may provide a source of intrinsic inhibition that contributes to the more selective tuning in broad-spiking cells. NEW & NOTEWORTHY The response properties of neurons in higher level regions of auditory cortex in songbirds are of fundamental interest because processing in such regions is essential for vocal learning and plasticity and for auditory perception of complex sounds. Within a region of secondary auditory cortex, neurons with narrow spikes exhibited high firing rates to playback of both tones and multiple conspecific songs, whereas broad-spiking neurons responded sparsely and selectively to both tones and songs.

scholarly journals Multimodal Medullary Neurons and Correlational Linkages of the Respiratory Network

1999 ◽  
Vol 82 (1) ◽  
pp. 188-201 ◽  
Author(s):  
Zhongzeng Li ◽  
Kendall F. Morris ◽  
David M. Baekey ◽  
Roger Shannon ◽  
Bruce G. Lindsey
Keyword(s):  
Firing Rate ◽  
Nucleus Tractus Solitarius ◽  
Motor Pattern ◽  
Sensory Modality ◽  
Spike Trains ◽  
Negative Feedback Regulation ◽  
Firing Rates ◽  
Respiratory Network ◽  
Cross Correlation Analysis ◽  
Stimulation Of

This study addresses the hypothesis that multiple sensory systems, each capable of reflexly altering breathing, jointly influence neurons of the brain stem respiratory network. Carotid chemoreceptors, baroreceptors, and foot pad nociceptors were stimulated sequentially in 33 Dial-urethan–anesthetized or decerebrate vagotomized adult cats. Neuronal impulses were monitored with microelectrode arrays in the rostral and caudal ventral respiratory group (VRG), nucleus tractus solitarius (NTS), and n. raphe obscurus. Efferent phrenic nerve activity was recorded. Spike trains of 889 neurons were analyzed with cycle-triggered histograms and tested for respiratory-modulated firing rates. Responses to stimulus protocols were assessed with peristimulus time and cumulative sum histograms. Cross-correlation analysis was used to test for nonrandom temporal relationships between spike trains. Spike-triggered averages of efferent phrenic activity and antidromic stimulation methods provided evidence for functional associations of bulbar neurons with phrenic motoneurons. Spike train cross-correlograms were calculated for 6,471 pairs of neurons. Significant correlogram features were detected for 425 pairs, including 189 primary central peaks or troughs, 156 offset peaks or troughs, and 80 pairs with multiple peaks and troughs. The results provide evidence that correlational medullary assemblies include neurons with overlapping memberships in groups responsive to different sets of sensory modalities. The data suggest and support several hypotheses concerning cooperative relationships that modulate the respiratory motor pattern. 1) Neurons responsive to a single tested modality promote or limit changes in firing rate of multimodal target neurons. 2) Multimodal neurons contribute to changes in firing rate of neurons responsive to a single tested modality. 3) Multimodal neurons may promote responses during stimulation of one modality and “limit” changes in firing rates during stimulation of another sensory modality. 4) Caudal VRG inspiratory neurons have inhibitory connections that provide negative feedback regulation of inspiratory drive and phase duration.

scholarly journals Statistical assessment of the stability of neural movement representations

2011 ◽  
Vol 106 (2) ◽  
pp. 764-774 ◽  
Author(s):  
Ian H. Stevenson ◽  
Anil Cherian ◽  
Brian M. London ◽  
Nicholas A. Sachs ◽  
Eric Lindberg ◽  
...  
Keyword(s):  
Primary Motor Cortex ◽  
Tuning Curve ◽  
Modulation Depth ◽  
Measurement Noise ◽  
Neural Representation ◽  
Experimental Conditions ◽  
Sensory Stimuli ◽  
Tuning Curves ◽  
Dynamic Tuning ◽  
Preferred Direction

In systems neuroscience, neural activity that represents movements or sensory stimuli is often characterized by spatial tuning curves that may change in response to training, attention, altered mechanics, or the passage of time. A vital step in determining whether tuning curves change is accounting for estimation uncertainty due to measurement noise. In this study, we address the issue of tuning curve stability using methods that take uncertainty directly into account. We analyze data recorded from neurons in primary motor cortex using chronically implanted, multielectrode arrays in four monkeys performing center-out reaching. With the use of simulations, we demonstrate that under typical experimental conditions, the effect of neuronal noise on estimated preferred direction can be quite large and is affected by both the amount of data and the modulation depth of the neurons. In experimental data, we find that after taking uncertainty into account using bootstrapping techniques, the majority of neurons appears to be very stable on a timescale of minutes to hours. Lastly, we introduce adaptive filtering methods to explicitly model dynamic tuning curves. In contrast to several previous findings suggesting that tuning curves may be in constant flux, we conclude that the neural representation of limb movement is, on average, quite stable and that impressions to the contrary may be largely the result of measurement noise.

Bursts and recurrences of bursts in the spike trains of spontaneously active striate cortex neurons

1985 ◽  
Vol 53 (4) ◽  
pp. 926-939 ◽  
Author(s):  
C. R. Legendy ◽  
M. Salcman
Keyword(s):  
Standard Deviation ◽  
Spike Train ◽  
Striate Cortex ◽  
Quantitative Measure ◽  
Spike Trains ◽  
Spike Rate ◽  
Occurrence Rate ◽  
Implanted Electrodes ◽  
Firing Rates ◽  
The Mean

Simultaneous recordings were made from small collections (2-7) of spontaneously active single units in the striate cortex of unanesthetized cats, by means of chronically implanted electrodes. The recorded spike trains were computer scanned for bursts of spikes, and the bursts were catalogued and studied. The firing rates of the neurons ranged from 0.16 to 32 spikes/s; the mean was 8.9 spikes/s, the standard deviation 7.0 spikes/s. Bursts of spikes were assigned a quantitative measure, termed Poisson surprise (S), defined as the negative logarithm of their probability in a random (Poisson) spike train. Only bursts having S greater than 10, corresponding to an occurrence rate of about 0.01 bursts/1,000 spikes in a random spike train, were considered to be of interest. Bursts having S greater than 10 occurred at a rate of about 5-15 bursts/1,000 spikes, or about 1-5 bursts/min. The rate slightly increased with spike rate; averaging about 2 bursts/min for neurons having 3 spikes/s and about 4.5 bursts/min for neurons having 30 spikes/s. About 21% of the recorded units emitted significantly fewer bursts than the rest (below 1 burst/1,000 spikes). The percentage of these neurons was independent of spike rate. The spike rate during bursts was found to be about 3-6 times the average spike rate; about the same for longer as for shorter bursts. Bursts typically contained 10-50 spikes and lasted 0.5-2.0 s. When the number of spikes in the successively emitted bursts was listed, it was found that in some neurons these numbers were not distributed at random but were clustered around one or more preferred values. In this sense, bursts occasionally "recurred" a few times in a few minutes. The finding suggests that neurons are highly reliable. When bursts of two or more simultaneously recorded neurons were compared, the bursts often appeared to be temporally close, especially between pairs of neurons recorded by the same electrode; but bursts seldom started and ended simultaneously on two channels. Recurring bursts emitted by one neuron were occasionally accompanied by time-locked recurring bursts by other neurons.

Response to Motion in Extrastriate Area MSTl: Disparity Sensitivity

1999 ◽  
Vol 82 (5) ◽  
pp. 2462-2475 ◽  
Author(s):  
Satoshi Eifuku ◽  
Robert H. Wurtz
Keyword(s):  
Receptive Field ◽  
Tuning Curve ◽  
Receptive Fields ◽  
Relative Difference ◽  
Moving Object ◽  
Absolute Difference ◽  
Stimulus Motion ◽  
Temporal Area ◽  
Moving Stimuli ◽  
Medial Superior Temporal

Many neurons in the lateral-ventral region of the medial superior temporal area (MSTl) have a clear center surround separation in their receptive fields. Either moving or stationary stimuli in the surround modulates the response to moving stimuli in the center, and this modulation could facilitate the perceptual segmentation of a moving object from its background. Another mechanism that could facilitate such segmentation would be sensitivity to binocular disparity in the center and surround regions of the receptive fields of these neurons. We therefore investigated the sensitivity of these MSTl neurons to disparity ranging from three degrees crossed disparity (near) to three degrees uncrossed disparity (far) applied to both the center and the surround regions. Many neurons showed clear disparity sensitivity to stimulus motion in the center of the receptive field. About [Formula: see text] of 104 neurons had a clear peak in their response, whereas another [Formula: see text] had broader tuning. Monocular stimulation abolished the tuning. The prevalence of cells broadly tuned to near and far disparity and the reversal of preferred directions at different disparities observed in MSTd were not found in MSTl. A stationary surround at zero disparity simply modulated up or down the response to moving stimuli at different disparities in the receptive field (RF) center but did not alter the disparity tuning curve. When the RF center motion was held at zero disparity and the disparity of the stationary surround was varied, some surround disparities produced greater modulation of MSTl neuron response than did others. Some neurons with different disparity preferences in center and surround responded best to the relative disparity differences between center and surround, whereas others were related to the absolute difference between center and surround. The combination of modulatory surrounds and the sensitivity to relative difference between center and surround disparity make these MSTl neurons particularly well suited for the segmentation of a moving object from the background.

Processing of form and motion in area 21a of cat visual cortex

1993 ◽  
Vol 10 (1) ◽  
pp. 93-115 ◽  
Author(s):  
B. Dreher ◽  
A. Michalski ◽  
R. H. T. Ho ◽  
C. W. F. Lee ◽  
W. Burke
Keyword(s):  
Spatial Organization ◽  
Receptive Fields ◽  
Direction Selectivity ◽  
Orientation Tuning ◽  
Area 17 ◽  
Horizontal Strip ◽  
Tuning Curves ◽  
Mean Width ◽  
Area 21A ◽  
The Mean

AbstractExtracellular recordings from single neurons have been made from presumed area 21a of the cerebral cortex of the cat, anesthetized with N2O/O2/sodium pentobarbitone mixture. Area 21a contains mainly a representation of a central horizontal strip of contralateral visual field about 5 deg above and below the horizontal meridian.Excitatory discharge fields of area 21a neurons were substantially (or slightly but significantly) larger than those of neurons at corresponding eccentricities in areas 17, 19, or 18, respectively. About 95% of area 21a neurons could be activated through either eye and the input from the ipsilateral eye was commonly dominant. Over 90% and less than 10% of neurons had, respectively, C-type and S-type receptive-field organization. Virtually all neurons were orientation-selective and the mean width at half-height of the orientation tuning curves at 52.9 deg was not significantly different from that of neurons in areas 17 and 18. About 30% of area 21a neurons had preferred orientations within 15 deg of the vertical.The mean direction-selectivity index (32.8%) of area 21a neurons was substantially lower than the indices for neurons in areas 17 or 18. Only a few neurons exhibited moderately strong end-zone inhibition. Area 21a neurons responded poorly to fast-moving stimuli and the mean preferred velocity at about 12.5 deg/s was not significantly different from that for area 17 neurons.Selective pressure block of Y fibers in contralateral optic nerve resulted in a small but significant reduction in the preferred velocities of neurons activated via the Y-blocked eye. By contrast, removal of the Y input did not produce significant changes in the spatial organization of receptive fields (S or C type), the size of the discharge fields, the width of orientation tuning curves, or direction-selectivity indices.Our results are consistent with the idea that area 21a receives its principal excitatory input from area 17 and is involved mainly in form rather than motion analysis.

Properties of proprioceptive neurons in the cuneate nucleus of the cat

1987 ◽  
Vol 57 (4) ◽  
pp. 938-961 ◽  
Author(s):  
D. J. Surmeier ◽  
A. L. Towe
Keyword(s):  
Spectral Analysis ◽  
Muscle Spindle ◽  
Receptive Fields ◽  
Spike Trains ◽  
Cuneate Nucleus ◽  
Periodic Patterns ◽  
Class A ◽  
Periodic Discharge ◽  
Periodic Components ◽  
Spindle Fibers

Fifty-two slowly adapting proprioceptive neurons in the cuneate nucleus of chloralose-anesthetized cats were studied. Recordings were made from 3 mm rostral to the obex to 5 mm caudal. The highest densities of proprioceptive neurons were found above and more than 3 mm caudal to the obex. Analysis of the spike trains produced with the forelimb held fixed revealed three basic periodic patterns. Neurons exhibiting these patterns were partitioned into three groups, referred to as the A, B, and C classes. Class A neurons (42%; 22/52) produced regular spike trains that were qualitatively similar to muscle spindle fibers. Interval distributions for this class were typically unimodal and slightly positively skewed. Adjacent intervals were frequently positively correlated. Spectral analysis suggested that 91% of class A spike trains had one to two periodic components. Class B neurons (21%; 11/52) had additional spikes interposed in their periodic discharge; these "interrupting" spikes did not significantly alter the timing of the dominant periodic discharge. Interval distributions were typically bimodal and adjacent intervals were negatively correlated. Spectral analysis suggested that two or more periodic components were present in their spike trains. Class C neurons (36%; 26/52) had spike trains with a basic rhymicity, but when this specific discharge was interrupted, the subsequent interval was near modal length; thus, they were "reset." Interval distributions were usually multimodal and adjacent intervals were frequently negatively correlated. Spectral analysis suggested that C spike trains usually had four or more periodic components. Estimates of information-carrying capacity of each class using a mean rate code and those of primary muscle spindle fibers suggested that a sizable information loss may occur in synaptic transmission. This potential loss was smaller for A-neurons (40%) than for B- (69%) or C-neurons (64%). Electrical stimulation of cutaneous structures influenced 55% (22/52) of the sample. All were members of the B and C classes. Responses were typically biphasic. The cutaneous receptive fields nearly always included a portion of the forepaw. No relationship was found between movement sensitivity and receptive field topography. Contralateral input was found in half (10/20) the neurons tested.

Inferior colliculus. II. Development of tuning characteristics and tonotopic organization in central nucleus of the neonatal cat

1975 ◽  
Vol 38 (5) ◽  
pp. 1208-1216 ◽  
Author(s):  
L. M. Aitkin ◽  
D. R. Moore
Keyword(s):  
Inferior Colliculus ◽  
Tuning Curve ◽  
External Auditory Meatus ◽  
Auditory Pathway ◽  
Central Nucleus ◽  
Synaptic Density ◽  
Tonotopic Organization ◽  
Tuning Curves ◽  
Sharp Form ◽  
Cochlear Development

Tuning curves were measured for 65 units in the inferior colliculus of seven anesthetized kittens aged from 6 to 28 days. At 2 days of age the inferior colliculus was divisible into central, pericentral, and external nuclei. Evidence was found for broader tuning curves to occur in the pericentral nucleus compared with the central nucleus, as has been observed in the adult. The middle ear was filled with serous fluid to 6 days, while the external auditory meatus remained collapsed until 10 days. Central nucleus tuning curves in kittens were relatively flat with high thresholds. Best-frequency thresholds diminished from a mean of near 100 dB SPL at 6-11 days to near 50 dB in the adult. The marked drop in thresholds between days 22 and 21 led to the adoption of the sharp form of tuning curve common for adults. Tonotopic organization of the central nucleus was clear at day 11. Speculations were advanced about the dependence of central auditory maturations on cochlear development, axon myelination in the auditory pathway, and changes in synaptic density as a function of age.

scholarly journals Automatic Spike Sorting Using Tuning Information

2009 ◽  
Vol 21 (9) ◽  
pp. 2466-2501 ◽  
Author(s):  
Valérie Ventura
Keyword(s):  
Maximum Likelihood ◽  
Expectation Maximization ◽  
Poisson Processes ◽  
Spike Sorting ◽  
Maximum Likelihood Algorithm ◽  
Firing Rates ◽  
Novel Approach ◽  
Misclassification Rates ◽  
Available Information ◽  
Spike Waveforms

Current spike sorting methods focus on clustering neurons' characteristic spike waveforms. The resulting spike-sorted data are typically used to estimate how covariates of interest modulate the firing rates of neurons. However, when these covariates do modulate the firing rates, they provide information about spikes' identities, which thus far have been ignored for the purpose of spike sorting. This letter describes a novel approach to spike sorting, which incorporates both waveform information and tuning information obtained from the modulation of firing rates. Because it efficiently uses all the available information, this spike sorter yields lower spike misclassification rates than traditional automatic spike sorters. This theoretical result is verified empirically on several examples. The proposed method does not require additional assumptions; only its implementation is different. It essentially consists of performing spike sorting and tuning estimation simultaneously rather than sequentially, as is currently done. We used an expectation-maximization maximum likelihood algorithm to implement the new spike sorter. We present the general form of this algorithm and provide a detailed implementable version under the assumptions that neurons are independent and spike according to Poisson processes. Finally, we uncover a systematic flaw of spike sorting based on waveform information only.

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