Methods

EXTRACELLULAR RECORDING AND ANALYSIS OF NEURONAL ACTIVITY

 

Abstract

In this chapter I discuss the relationship between action potentials recorded intracellularly and their extracellular traces. The main factors underlying the variance of the extracellular traces of the same intracellular event will be considered. The transfer function, which make us able to infer from the extracellular signal to the intracellular sources, is a key of developing reliable single unit detection methods. One such an attempt is the spatial clustering method, based on using the silicon multiprobe, is demonstrated here. Having discussed the problems and solutions of multiunit clustering I can introduce the parallel spike trains as spike trains generated by isolated individual neurons. From this point I will be focusing on pyramidal cell interactions. For investigating higher order spike statistics within parallel spike trains two methods of sequence detection (the template matching and joint probability mapping) and corresponding statistical tests (Monte Carlo statistics and Fisher's exact probability test) will be described in details.

 

THE NEED FOR HIGH RESOLUTION IMAGING OF NETWORK ACTIVITY

In the brain, there is both large scale and small scale organization, and different functions take place on higher and lower levels. It is generally acknowledged that computational rules of the brain can be best understood by studying neuronal activity at the network (submillimeter) level (Petsche et al., 1984; Churchland and Sejnowski, 1992). This is the domain where emerging properties of neuronal interactions can be measured and models testing the biologically based hypotheses can be developed. Despite this recognition, this is the level where experimental progress has been slow. A combined effort at the biological, engineering and analysis levels is required to reveal computational rules of neuronal networks.

A straightforward approach to examine the sources of the extracellularly recorded population (field) events is to simultaneously record from teneously record from ten to one hundred of neurons. Electrical recording from deep brain structures using wire electrodes is one of the oldest methods in neuroscience. Local field potential measurements or "micro-EEG" (Petche et al., 1984) combined with recording of neuronal discharges is the best experimental tool available to study the average behavior of small population of neurons. To a large extent, the extracellular current flow will provide us information about the cooperating inputs onto the recorded cell population. In turn, recording unit activity (i. e., the extracellular action potentials) from the same population of cells will provide information about the output function. When both types of information are available, the influence of structural properties such as cortical lamination, distribution, size and network connectivity of neural elements and cytoarchitectonic peculiarities of the electrical features may be determined and one may begin to assess the input-output transformation by the neuronal network. To achieve this goal, a large number of recording points within a small volume of brain tissue is required for high spatial resolution and for making interpretation of the underlying cellular events possible.

 

SLOW FIELDS AND UNIT ACTIVITY: THE SOURCE OF EXTRACELLULAR CURRENT FLOW

Membrane cure currents generated by neurons pass through the extracellular space. These currents can be measured by electrodes placed outside the neurons. The field potentials (local mean field) recorded at any given site reflect the linear sum of field generated by current sources (current from the intracellular space to the extracellular space) and sinks (current from the extracellular space to the intracellular space) distributed along multiple cells. If the electrode is placed very close to a neuron, the extracellular currents will provide information about this given cell and its immediate neighbors.

The largest amplitude intracellular event is the fast sodium spike, referred to as the fast (Na+) action potential intracellularly and as unit activity extracellularly (Fig. 2.1). Due to the low-pass (capacitive) filtering properties of the extracellular environment, the amplitude of unit activity decreases substantially with distance between the recording site and the cell membrane. This is the main reason why contribution of fast action potentials to the field activity recorded with larger electrodes (EEG) is negligible. However, when action potentials from a large number of neighboring neurons occur within a short time window, e. g., in response to electrical stimulation of afferents or during epileptic activity, these "populatation spikes" can be recorded with relatively large size electrodes and in a larger volume (Andersen et al., 1966).

Fig. 2.1. Relationship between intracellularly and extracellularly recorded action potentials. A hippocampal CA1 pyramidal cell was impaled in the soma and a 20 µm wire electrode was placed close to the perisomatic region (scheme in A). Intrasomatic current injection (current) induced a train of action potentials which were faithfully recorded by the extracellular electrode (wide-band, 1 Hz to 5 kHz, extra). (B) Averaged intracellular and extracellular action potentials. The first to the third action potentials (1, 2, 3) after the current onset were averaged separately. Note that the serial effect is clearly reflected by the late components of the extracellular units. (C) Amplitude decrement of successive fast spikes recorded intrasomatically and extracellularly (percent of first spike). Note that the amplitude of the extracellularly recorded spikes was attenuated, whereas intrasomatic action potentials were only slightly affected. Vertical bars: standard error of the mean. (D) The extracellular signal was superimposed on the first derivative (1st der) of the intrasomatically recorded action potentialntial. The good match suggests that the extracellular electrode was placed close to the cell body. (From Buzsáki et al., 1996).

 

 

Besides unit activity, extracellular electrodes may provide information about other intracellular events as well, although extracellular measurements rarely allow monitoring of slow intracellular events of single neurons. Instead, these slow events typically reflect cooperative activity in neuronal populations (micro or macro electroencephalogram, EEG). Until recently, synaptic activity (IPSPs and EPSPs) has been viewed as the exclusive source of extracellular current flow or EEG. This notion stems from the recognition that for the effective summation of extracellular currents from numerous individual compartments, the events must be relatively slow. Progress in this field during the past decade, however, revealed numerous sources of relatively slow membrane potential fluctuations, not directly associated with synaptic activity. Such non-synaptic events may also significantly contribute to the generation of local field potentials. These include spike afterpotentials, particularly the slow and long-lasting calcium-mediated potassium current and voltage-dependent oscillations observed in various neurons. Field potential measurements provide an excellentllent experimental tool for assessing the spatio-temporal cooperativity of afferent, associational and local operations in a given structure at high temporal resolution. However, without a mechanistic description of the underlying neuronal processes, the field potential remains a gross correlate of brain activity rather than a predictive descriptor of the specific functional/anatomic alterations. Field potentials, however, become very valuable when action potentials of a representative number of principal cells and interneurons are simultaneously available. Field potentials, for example, provide information about biologically relevant time epochs within which cooperative operations should be searched for (e. g., theta and gamma frequency oscillations in the hippocampus). The generation of extracellular slow fields have been the subject of several recent reviews (Petsche et al., 1984; Pedley and Traub, 1990; Buzsáki and Traub, 1996).

 

EXTRACELLULAR RECORDING OF ACTION POTENTIALS

Traditional models of neuronal function state that fast (sodium) spikes are generated in the axon hillock or axon initial segment and passively propagate back to the dendrites. The large inward current associated with the spike is reflected by a negative change of the extracellular voltage at the level of l of the axon initial segment/cell body accompanied by a smaller amplitude, extracellular positive deflection out in the dendritic regions (Fig. 2.2).

Fig. 2.2. Propagation speed of sodium spike in a CA1 pyramidal cells in vivo. Averaged action potentials (n=256) from the four recording electrodes from cells A and B are shown at left and right, respectively. Filter settings: 1-5 kHz; sampling rate: 20 kHz. (Inset): Hypothesized relationship between recording sites (25-m m intersite intervals) and spatial position of two simultaneously recorded cells, drawn from two filled cells. (C and D) Details of the action potential peaks shown in A and B, respectively. Note that in A spikes occur first at the site with the largest amplitude action potential (site 1: putative somatic region of the neuron). Such a relationship between spike amplitude and peak latency was typical in the majority of neurons. In neuron B (a rare case), the spike occurred simultaneously or earlier at site 1 than at the site with the largest amplitude action potential (site 2). Spike at site 1 may reflect sodium spike initiation at the axon initial segment (From Buzsaki et al., 1996).

The extracellular record is typically biphasic and is interpreted as an indication that the recording tip is near the cell body (Frank 1955; Terzuolo and Araki 1961). Direct demonstration of the relationship between the action potential and extracellular "unit" activity derives from simultaneous recording of the intra- and extracellular signals from the same cell (Fig. 2.1). It is quite obvious from the recordings that there are differences between the forms of the intracellular and extracellular signals. First, the amplitude of the extracellular signal is one or two orders of magnitude smaller. Second, the duration of the extracellular spike is significantly shorter than that of the action potential recorded intracellularly. Third, the overall shape of the extracellular signal is quite different than the intracellular one. Nevertheless, it is of utmost importance that the intracellularly and extracellularly measured parameters of the action potentials quite reliably correlate, indicating that some of the intracellular changes may be inferred from a proper quantitative analysis of the extracellular signal. One such promising possibility is that the post-spike part of the extracellular unit may be used to assess e. g., spike afterhyperpolarization and GABAA-mediated recurrent inhibition.

 

Spike Propagationion in the Extracellular Space

Due to the low-pass filtering property of the extracellular space, the amplitude of the extracellularly recorded unit activity attenuates quite rapidly. Although the neuron-electrode distance for efficient recording of unit activity varies substantially from cell to cell (see below), certain generalizations can be made from measurements made on neocortical pyramidal cells (Fig. 2.3A). A silicon probe with a diamond-shaped recording site configuration ("tetrode") was used to map the isopotential contours around a spontaneously active pyramidal cell in the anesthetized rat. The probe was advanced in small steps in the vicinity of a single neuron and the amplitudes of the successively recorded spikes were measured. These data-generated plots were then compared with contour maps generated by calculating the action-potential generated voltage by a model neuron (Fig. 2.3B). These early experiments with multiple-site probes suggested that a) imaging the location of the action potential generation site is feasible using three or more recording sites with adequate signal-to-noise ratio, b) the site spacings for simultaneous recordings from the same cell should preferably be less than 50 µm for cortical pyramidal cells and c) temporal coherency of both unit potentials and low-frequency noise between adjacent recordings sites can be employed in signal l processing algorithms to improve single-unit sorting and signal-to-noise ratios. The use of multiple recording possibilities from the same neuron provided new methods for improving single unit sorting based on the temporal coherence of spikes from closely-spaced recording sites (Drake et al., 1988; McNaughton et al., 1983; Reece and O'Keefe, 1989).

Fig. 2.3. Extracellular propagation of the action potential. (A) Successive recordings from a neocortical pyramidal cell using a 4-site recording silicon probe (left). The sites have a diagonal spacing of 42 µm center-to-center. (B) Top. Extracellular potential contour derived from the data in A. Lower plot. Theoretical plot generated from simulated data as the probe advanced by a point-source model neuron. An outline of the probe and the 4 recording sites are shown on both plots. Isopotential lines are shown in microvolts. (From Drake et al., 1988).

 

 

Active Backpropagation of Action Potentials in Dendrites: Origin of Complex-spike Bursts

Neurons are not point sources of extraces of extracellular current generation but complex three-dimensional structures. Consequently, the somata of neurons cannot be regarded as the sole source of action potentials. Supporting previous suggestions (Llinas and Nicholson, 1971), recent in vitro work provided evidence that the dendritic membrane can exhibit electroresponsive properties and actively support propagation of action potentials in dendritic compartments (Huguenard et al., 1989; Regehr et al., 1993; Stuart and Sakman, 1994; Spruston et al., 1995; Magee and Johnston, 1995). Specifically, simultaneous recordings from the soma and dendrites of neocortical and hippocampal pyramidal cells and substantia nigra neurons in vitro suggest that sodium spikes, initiated in the axon initial segment, actively backpropagate into the distal dendrites (Stuart and Sakman, 1994; Spruston et al., 1995; Häusser et al., 1995). The in vitro measurements are also supported by experiments carried out in the freely moving rats. Simultaneous measurements from both soma and dendrites in hippocampal and neocortical pyramidal cells show that the action potential triggered at the action initiation site below the soma (putative axon initial segment) and travels back to the dendrites at 0.5 to 2 m/sec (Fig. 2.2; Buzsáki et al., 1996). These observations have important implications for the extracellular measurement and selection of unit activity. Importantly, dendritic sodium conductances may be affected by both the intrinsic activity of the recorded neuron and interneuron-mediated inhibition of the dendrites. The attenuation or failure of the active dendritic propagation of the action potential, in turn will reduce the size of the extracellularly recorded unit activity. Briefly, a simple two-dimensional neuron model with a strong current sink representing the soma and a current source representing a single dendritic branch imposes limitations on the accuracy of unit sorting algorithms based on stationary models of spike generation. This difficulty poses problems for multiunit spike separation, especially for bursting neurons.

Repetitive spikes with decrementing amplitude occur spontaneously during consummatory behaviors and slow wave sleep in hippocampal pyramidal cells and are termed "complex-spike" bursts (Ranck, 1973). A possible mechanism for the generation of the decrementing amplitude units during the burst is illustrated in Fig. 2.4. Linear arrays of silicon probes (see below) with 25-µm recording intervals were closely positioned to CA1 or CA3 pyramidal neurons, so that sodium spikes could be recorded from the same cell(s) at 4 recording sites. The amplitude decrement of spikes during a complex-spike burst was frequency-dependent (Ranck, 1973); spikes occurring at shorter intervals were attenuated more than spikes with h longer interspike intervals. However, the degree of spike amplitude attenuation strongly depended on the recording site. Close to the cell body, only a moderate amplitude decrement was observed within a complex-spike burst (Fig. 2.2, site 4). At the same time, the amplitude attenuation at more distal recording sites (dendritic locations) was often substantial (Fig. 2.2, sites 2 and 3). Late occurring action potentials at dendritic recording sites were sometimes buried in the background noise. An interpretation of this observation is that "complex-spikes" in the extracellular field emerge because the extracellular electrode integrates electrical activity over a large segment of the somadendritic surface and because spikes occurring in fast succession may fail to invade the dendrites equally (Buzsáki et al., 1996). An important practical implication of these experiments is that the magnitude of the amplitude decrement during a complex-spike burst depends on the relative distance of the recording electrode from the soma of the neuron. The closer the electrode to the neuron the larger the amplitude dectement is. Thus, the amplitude ratio between the two recording electrodes will be biased toward the more distant electrode. The consequence of all this is that spike sorting algorithms based on spatial localization of the spike may regard the successive spikes of a complex-spike series as separate neurons.

Fig. 2.4. Attenuation of sodium spike propagation in CA1 pyramidal cell dendrites during complex-spike bursts. (A) Complex-spike burst of 7 action potentials at the soma (filter: 0.1-5 kHz; sampling rate: 20 kHz). Right: hypothesized relationship between recording sites (25 µm intersite intervals) and the recorded CA3 pyramidal cell. Note amplitude decrement of successive actions potentials at recording sites 3, 2 and 1 (arrows in site 3). (B) Average amplitude decrease of action potentials during complex-spike bursts in a group of 7 CA3 pyramidal cells. Note that spike amplitude attenuation is larger at the more distal (dendritic) locations (sites 1, 2 and 3) than at the soma (site 4). (C) Relative spatial location of successively occurring action potentials in the extracellular space. "Spatial location" was calculated by a cubic spline interpolation of the spike amplitudes at each of the four recording sites and the resulting values were plotted as a function of spike amplitude for successive spikes (1 to 4). Mean values for locations are shown by the respective larger symbols next to the ordinate. Note that the spatial location of later occurring action potentials of the complex-spike burst is closer to the somatic region (somasoma). den, apical dendrites. In effect, unit sorting programs based on spatial localization of unit activity will classify the successively emitted action potentials from the same neuron as activity of several cells. (From Buzsáki et al., 1996).

 

 

 

Sources of Amplitude- and Shape-variations of the Extracellular Unit

Of the many parameters that may influence the amplitude and waveform of the extracellular unit response, properties of the neuron membrane, the three-dimensional structure of the cell and the extracellular milieu appear most important. It follows that the strategies of extracellular recordings should be adapted both to the anatomical region and to the neuron type in question.

 

Cell Lipid Membrane - Capacitive Differentiation

The lipid bilayer of the neuronal membrane functions as a series capacitance between the intracellular signal and the extracellular recording electrode. This capacitance is believed to determine the primary shape of the extracellular potential. A strong support for the hypothesis of capacitive differentiation comes from thcomes from the observation that the first derivative of the intracellular action potential is very similar to the extracellularly recorded (wide band) unit (Fig. 2.1). Given this reliable correlation, the rise and fall time of the action potential can be predicted from the extracellular trace. It is also noteworthy from these simultaneous recordings that other parameters, such as the spike after-hyperpolarization may also be inferred from the extracellular record.

The capacitive differentiation by the lipid membrane should also affect the amplitude of the extracellular unit potential. Faster rising-falling action potentials should generate larger amplitude extracellular units than wide action potentials. This hypothesis has yet to be verified. However, this prediction is supported by the significantly larger amplitude derivatives of the action potentials of the majority of hippocampal interneurons (Fig. 2.5). In general, the duration of the action potential is considerably shorter in cortical interneurons than in pyramidal cells, and this distinction is often used as a criteria for the extracellular identification of interneurons (Buzsáki and Eidelberg, 1982). Unfortunately, this criterion is not absolute, since the action potential duration of basket cells and hippocampal pyramidal neurons may be quite similar. Therefore, although short duration extracellular units may positivively identify several interneuronal types, this criterion alone is not sufficient for all types (Freund and Buzsáki, 1996).

 

Fig. 2.5. Intracellularly recorded, averaged spikes (upper row) from a CA1 pyramidal cell and different types of interneurons (Sik et al., 1995) and the first derivatives of the action potentials (second row). On the basis of the similarity of the extracellularly recorded unit and the first derivative of the intracellular action potential (see Fig. 2.1), the shape and duration of extracellular units recorded from these different interneuron types are expected to be characteristically different. The action potential from the CA1 pyramidal cell was recorded from the apical dendritic shaft.

 

 

 

Membrane potential

The momentary polarization level of the cell membrane has a significant effect on the amplitude of the action potential. When a neuron discharges from a relatively more depolarized membrane potential, the action potential is proportionally smaller. Such an amplitude rn amplitude reduction is also reflected by the extracellularly recorded units. The amplitude reduction may be substantial when e. g., a pyramidal cell fires a high-threshold calcium spike crowned with fast, sodium spikes. A large "ramp-like" depolarization of the neuron will have a similar effect. For example, hippocampal pyramidal cells increase their discharge rate several-fold when the rat crosses the "spatial field" of the neuron. As shown experimentally, the amplitude decrement of the unit shows a predictive relationship with behavior. The amplitude of the spatial unit is smaller in the center than at the periphery of the spatial field (Wilson, personal communication). A reasonable interpretation of the amplitude decrease is that the neuron is maximally depolarized in the center of the spatial field.

Conversely, hyperpolarization of the membrane results in an increase of the amplitude of the extracellular units. Amplitude histograms of multiple unit activity from the ventrolateral nucleus of the thalamus revealed larger amplitude units during slow wave sleep than in the awake state. Recording from putative single units with sharp tungsten electrodes (> 5 MOhm) showed a consistent amplitude increase during sleep (our unpublished findings). A likely interpretation of these observation is that during sleep spindles thalamocortical cells are rhythmically hyperpolarized by the inhihibitory reticular nucleus neurons and discharge low threshold calcium spikes (Steriade and Llinas, 1988; Sawyer et al., 1994), whereas in the awake animal they typically discharge single or repetitive "simple" sodium spikes, initiated above the resting membrane potential.

 

Dendritic morphology

This variable is perhaps the most important for the design of the recording electrode configuration. As discussed above, the voltage sensed by the extracellular electrode depends strongly on the direction and density of current flow. Consequently, neurons with parallel dendrites should generate larger amplitude currents in the extracellular space than cells with radially running dendrites. Although this relationship has long been tacitly acknowledged, formal experiments comparing extracellular activity recorded from different cell types by the same recording electrode are rare. Cortical pyramidal cells and cerebellar Purkinje neurons have a large apical dendrite and therefore a very large part of the current flow in the perisomatic region points to the same direction. The result is a large and dense extracellular current flow, an optimal condition for extracellular recording. The unidirectional dendritic architecture of cortical pyramidal cells is the explanation why juxtadendritic action potentials ials can be recorded several hundred µm from the cell body (Fig. 2.2). Parvalbumin-immunoreactive basket cells and chandelier cells in the hippocampus are similar in shape to pyramidal cells (Li et al., 1992; Gulyas et al., 1993; Buhl et al., 1994; Sik et al., 1995). Although, in contrast to pyramidal cells, several apical dendrites emanate from the soma, they run in the same direction and therefore the currents generated by the traveling action potentials in the different dendrites sum linearly in the extracellular space. This allows for simultaneous recording of relatively large amplitude units from both soma and dendrites of these neurons (Fig. 2.6).

Fig. 2.6. Simultaneous recordings from the somatic and dendritic regions of two putative basket cells in the CA3c pyramidal layer. (A) Parvalbumin-immunoreacted section showing the track made by the silicon probe. The arrows indicate the 4 recordings sites (25 µm intervals) in the CA3c pyramidal layer. Inset: Larger magnification of the track. Arrowheads point to parvalbumin-positive interneurons. (B) Camera lucida reconstruction of a single parvalbumin-immunoreactive neuron from a neighboring section. Relative positions of the recordings sites are indicated by arrows. (C) Wide band recording ing (1 Hz-5 kHz) of field activity during walking. Two different units (a and b) are revealed by the 4-site recording probe. (D) Evoked responses of the units in response to perforant path (PP) stimulation. Upper trace wide band (1 Hz-5 kHz), lower traces high-pass filtered (0.5-5 kHz). p, multiple unit discharges of putative pyramidal cells.

 

 

Many neurons, however, possess radially projecting dendrites. Consequently, the action potential, emanated from the soma, travels into various directions. The small amplitude multiple dipoles, created by the action potentials traveling somatofugally in the various dendrites, therefore tend to diminish, rather than enhance, each other in the extracellular space. The result is a small amplitude extracellular unit due to the "closed" field generated by the radially running currents. This has two consequences for extracellular recordings. First, smaller amplitude action potentials will be generated by these neurons and therefore the recording electrode should be placed closer to the cell body during the experiment. Second, less number of neurons can be recorded by the same size electrode than, for example, in the pyramidal layers of the neocortex or hippocampus. Figure 7 illustrates these assumptions. In this experiment the same kind of sili silicon probe as used in Figs. 4 and 5 was placed in the hilar region of the hippocampal dentate gyrus. Despite of close spacing of the recording sites (25 µm), each site recorded a different neuron. This physiological observation is congruent with the non-pyramidal shape of these cells (Amaral, 1978). Another illustration is shown in Fig. 2.8. In this experiment the recording probe was placed into the dorsal part of the thalamus for simultaneous monitoring of the GABAergic neurons of the reticular nucleus and thalamocortical cells. Again, each of the four recording sites selected different cells with virtually no coherent action potentials at neighboring sites. Both reticular and thalamocortical cells have radially projecting dendrites (Fig. 2.8B), supporting the hypothesis that the small electrical fields generated by these neurons may be explained by their anatomical architecture.

Fig. 2.7. Simultaneous recordings of three interneurons (1 to 3) in the hilar region of the dentate gyrus using the same silicon probes as illustrated in Figs. 4 and 5. Interneurons 1 and 2 fired rhythmically during walking related theta activity, whereas interneuron 3 (antitheta cell) was completely suppressed. Diminished activity of the "theta-related" cells (1 and 2) coincided wit with the discharge of cell 3 (arrows). Note that action potentials are recognizable only in a single trace for each of the neuron. The small spatial extent of the units generated by these cells is congruent with their non-pyramidal shape (Amaral, 1978). (From Freund and Buzsáki, 1996).

 

 

Fig. 2.8. Simultaneous recordings from a reticular thalami (RT, 1) and thalamocortical neurons (th, 2, 3, 4) using the same silicon probe as illustrated in Figs. 4 to 6. (A) Two tracks are shown, in one (left) the probe remained in situ during the histological processing. Parvalbumin-immunoreacted section. White dots: recordings sites with 25 µm spacing. CC, corpus callosum. (B) Camera lucida reconstruction of a reticular thalami interneurons (RT) and two nearby thalamocortical cells from other intracellular experiments in vivo. Note radially directing dendrites of both cell types. (C) Rhythmic spike sequence of possibly single reticular thalami neuron (1) and multiple units from different thalamocortical cells (2-4) during sleep. Note that action potentials are recognizable only in a single trace for each of the neuron. The lack of intersite "cross-talk" and the small amplitude of the units is due to the stellatetellate dendritic shape of the recorded cells and the consequent small size of the electric field generated by the action potential.

 

Dendritic spike generation

A further difficulty that may be encountered during a physiological experiment is that the action potential initiation site may vary in the same neuron (Llinas and Nicholson, 1971; Traub and Miles, 1995). Although this is believed to happen only during pathological states in cortical principal cells, it appears that at least in some interneuron types in the cortex the action potential may emerge from one of the dendrites. Moreover, the action potential may emanate from various dendrites in an unpredictable fashion and it may not propagate equally to same set of dendrites from the different trigger sites. Therefore, the same interneuron can produce extracellular unit activity with varying shape, amplitude and spatial features (Fig. 2.9). The multiple site generation of action potentials throughout the dendritic arbor may also explain why the amplitude variability of extracellularly recorded interneurons sometimes exceeds 80% (our unpublished findings). Overall, these observations suggest that the methods and criteria worked out for unit sorting of pyramidal neurons may ns may not always apply to cortical interneurons. In effect, the currently available unit sorting methods based on spike shape differentiation will treat the different modes of firing of the same neuron as different cell clusters. The opposite technical problem may arise if neighboring neurons are electrically coupled or their action potentials temporally coincide. In this case, activity of several units may be falsely represented as a single unit cluster.

 

Evoked unit responses

A frequently used physiological method to identify units is to examine its evoked response properties. For example, neurons which project to known anatomical targets may be differentiated from those which do not by antidromic stimulation. Interneurons often fire repetitive spikes, whereas principal cells typically discharge only a single spike due to orthodromic stimulation. While these methods are quite reliable when a single cell is well-isolated, they are not foolproof when multiple unit activity is recorded by the electrode. Orthodromically evoked units are often much smaller in amplitude than "spontaneously" occurring units. The reason is that stimulation recruits strong feed-forward inhibition, which in turn, may shunt the dendritic membrane and attenuate the somadendritic backpropagation of the action potential (Fal (Fig. 2.10; Buzsáki et al., 1996), resulting in smaller amplitude extracellular unit. Synchronous activation of a large number of excitatory afferents by the simulation may also induce "ectopic" dendritic spike generation (Turner and Richardson, 1991), therefore the "spatial location" of the evoked and spontaneous units may be classified differently by the spike sorting algorithm. A useful method to circumvent these problems is to test each recognized units with an antidromic collision test. Albeit this approach may be time-consuming, it is perhaps the best on-line tool to separate projection and local circuit neurons. Unfortunately, the collision test is not particularly useful when neighboring neurons, such as hippocampal pyramidal cells, possess strongly overlapping targets.

Fig. 2.9. Possible dendritic generation of action potentials in interneurons. (A) Spontaneous activity of a CA1 trilaminar neuron in vivo (urethane anesthesia). The boxed area is shown at a higher resolution above. Open arrows indicate spike initiation. Note that spikes are not necessarily triggered at most depolarized levels of the membrane. The dissociation between local depolarizing potentials and the variability of the spike threshold suggests that fast spikes were initiated at location(on(s) other than the recording site. (B) Four-site recording (wire tetrode) from a stratum oriens interneuron in the CA1 region in the awake rat. Small (a, arrowheads) and large (b) spikes are present. (C) Spikes a and b at a faster scale. Note the double positive-going spikes in b. (D) Spatial clustering of spike parameters revealed two possible units (a and b). (E) However, cross-correlation between spikes a and b revealed a reliable refractory period, suggesting that both spikes were emitted by the same neuron. An alternative explanation is that spikes a and b were generated by interneurons coupled by gap junctions. (From Freund and Buzsáki, 1996).

 

 

Fig. 2.10. The amplitude of spontaneous and evoked action potentials are often different. The two spontaneously occurring spikes are "overshooting" (up to +10 mV), whereas the commissurally (com) evoked spike is "undershooting" (-5 mV). The likely explanation for the amplitude reduction of the evoked action potential is that commissural stimulation induces a strong feed-forward inhibition and a consequent increase in membrane conductance ("shunting") of the somathe soma and dendrite of the pyramidal neuron. The reduction of spike amplitude in the dendrite can be more substantial (not shown). Such amplitude reduction of the evoked spike may result in difficulties when evoked properties of units are compared to spontaneous activity in multiple unit recordings.

 

 

Properties of extracellular space

Changes in the extracellular milieu may also affect several parameters of the action potential. Ischemia, anoxia or epileptic activity change dramatically the Na+/K+ exchanger mechanism and build-up of extracellular K+ and glutamate may affect spike repolarization, afterhyperpolarization as well as the site of action potential generation (Fig. 2.11). Importantly in the present context, the spike initiation site of the action potential may migrate and extracellularly recorded spike shapes and spike locations will change accordingly. In short, modification of these factors may result in false identification of the altered spikes as new sets of neurons.

 

MULTIPLE SITE SILICON PROBES FOR PARALLEL RECORDING OF UNIT AND FIELD ACTIVITIES

Most knowledMost knowledge about the physiological function of the brain is based on studies of sequentially analyzed single site recordings. Although it has long been recognized that the computational power of complex neuronal networks cannot be fully recognized by studying the properties of single cells or activity of a few, selected sites, experimental access to the emergent properties of cooperating neurons has largely been impossible until quite recently. Direct investigation of the temporal dynamics of neuronal populations can only be based on simultaneous observation of large neuronal aggregates (Buzsáki et al., 1992; Wilson and McNaughton, 1993). The two critical requirements towards this goal are 1) placing a large number of recording electrodes in a small amount of tissue at the submillimeter range and 2) doing this without a significant tissue damage. These major requirements put constraints on wire electrodes due to the limited number of recording sites. Additional constraints are the number of lead wires, preamplifiers and the size of the head connector which could be carried by a behaving animal. Progress in this field has been accelerated by the development of silicon microtechnology-based multichannel recording devices (Kuperstein and Eichenbaum, 1985; Wise and Najafi, 1991).

In such silicon devices, the number of thin-film recording sites are defined lithographically usining the technology of integrated circuits (Fig. 2.12). The supporting silicon substrate is shaped using micromachining and a diffused boron etch-stop (Najafi, et al., 1985). The probe thicknesses are 10-15 µm with shank widths as narrow as 25 µm. Thus, these structures are capable of dimensions similar to those of a single cell. The tissue displacement for a single shank is typically less than for a single wire electrode even today, and each shank can carry many isolated sites. All dimensions (e.g., shank widths, thicknesses, site positions) can be controlled within ±1 µm or less.

Fig. 2.11. Simultaneous recordings from the somatic and dendritic regions of two CA1 pyramidal cell during epilepsy in the awake rat. (a) Complex-spike burst of 3 action potentials recorded from around the soma in cell A and a single spike recorded from cell B (filter: 0.1-5 kHz; sampling rate: 20 kHz). Right: hypothesized relationship between recording sites (25 µm intersite intervals) and the recorded pyramidal cells. (b) to (d). Behavior of the units during the initial part of stimulation-induced afterdischarge (tetanic stimulation of the perforant path). Neuron A was silent during this epoch. Note substantial amplitude decrement and failures of successive action potentials at recordinding site 3 (arrowheads in b). The amplitude attenuation of spike B at site 4 in (c) and (d) might be explained by the strong depolarization of the neuron brought about by the elevated extracellular K+. (e) Recovery, 5 min after the afterdischarge.

 

 

 

Fig. 2.12. Perspective view of a silicon micromachined multichannel microelectrode.

 

 

 

SINGLE CELL IDENTIFICATION IN PARALLEL-RECORDED MULTIUINT RECORDINGS

Parallel with the development of recording and storage methods, various computational algorithms have been devised for the decomposition of multiple unit data into single neuron events. Numerous spike recognition/sorting programs are available commercially, as well. Despite of major efforts in numerous laboratories, none of the currently available methods is sufficiently reliable. Typically, two types of errors are generated by both on-line and post-hoc methods: false identification and omission ernd omission errors. False unit identification error is inherent in methods based on amplitude and spike-shape recognition, since similar neurons equidistant from the recording site may generate spikes of identical amplitude and shape. This type of error is especially high when recordings are made from areas of high density of identical neurons, such as the pyramidal and granule cell layers of the hippocampus or the different neocortical layers. One efficient method to decrease false identification error is to use only the unit with the largest amplitude from each electrode. Although this selection increases single cell identification, it can occur only at the expense of drastically reducing the number of units for further analysis. Spike omission errors arise from the variability of the extracellularly recorded spike amplitude and shape of the same neuron, as discussed above. Spike omission errors therefore increase substantially with bursting cells and interneurons.

Current strategies for cell sorting of multiple unit data fall into two major categories. The first approach (amplitude/wave-shape recognition methods) is based on the presumption that different types of neurons generate different wave forms of spikes (Abeles and Goldstein, 1977). While this is true in general, neurons recorded by a single electrode are typically of the same type therefore have very similar shapes. The sececond approach requires simultaneous recordings from the same cells. The rationale behind this "spatial" method is that neurons which are at different distances from the recording sites will have different spike amplitude ratios when recorded from two or more sites simultaneously (McNaughton et al., 1983). Although two-channel recording enhances accuracy of unit separation, a more complete determination of point-like sources in Euclidean space requires at least four, preferably non-coplanar recording sites (Drake et al., 1988; Recce and O'Keefe, 1989). An obvious problem with the spatial method is that extracellularly recorded units reflect currents generated by both soma and dendrites and the variation of the dendritic spike amplitude modifies the virtual, extracellularly determined "site" of action potential generation (Fig. 2.4). Thus, both waveform recognition and spatial approaches have virtues and shortcomings. A combination of these approaches along with post-hoc tests (see below) may improve the accuracy of neuronal isolation.

To date, no reliability indices have yet been worked out for the quantitative assessment of false identification and omission errors generated by the different methods. Although independent measures are not available for matching the classified unit clusters with individual cells, it would nevertheless be important to examine how similarar or dissimilar clusters are generated by the methods used in different laboratories from the same database. Below, I will describe a spike sorting method which takes advantage of the metric spacing of the recordings sites of silicon probes. The reliability of the developed algorithm was examined by the spatially distinct field potentials generated by different afferents, prior to using the program for unit sorting.

 

Spatial Localization of Electrical Sources: Field Potentials

Before testing the spatial localization method on single neurons, I examined the reliability of the method with field potentials. This approach was used to provide an independent test for the reliability of spatial localization. In the hippocampus, three major intermittent field events, generated by the activity of separate afferents can be recognized: sharp waves (SPW) and two types of dentate spikes (DS1 and DS2; Buzsáki et al., 1983; Bragin et al., 1995). Previous current-source density analysis of these events revealed large sinks corresponding to the concerted activity of the Schaffer collaterals on CA1 pyramidal cells and of the medial and lateral perforant path fibers on the granule cells, respectively.

On the basis of the afferent projections to pyr to pyramidal cells and granule cells one can assume an invariant relationship between the anatomical sites and the calculated location of the physiological events in the Cartesian space. The amplitudes of these events recorded from each site of the probe can be represented by an amplitude vector. Each component of this amplitude vector reflects the field momentum for that channel. Assuming the homogeneity of the extracellular medium, the average of these field momentums covaries with the location of the field generation. Two functions, the "center of field" and "interpolated field position" have been devised to project the field momentums to an Euclidean coordinate system where one dimension corresponds to the spatial location of the field event and the other dimension indicates the average amplitude. In such a projection, each event is represented by a point in the location-amplitude space. A cluster of superimposed points of such a projection is assumed to be specific for the afferents involved in the generation of a particular field spike sequence.

 

 

Fig. 2.13. The main steps of the spatial separation of unit activity (a-i). The first five steps are identical to tal to those used in the localization of intermittent EEG events, as shown for field potentials in Fig. 2.14. (a) Co-occurring spike events are detected and sampled as wave shapes (1.2 msec samples). (b) The selected spike shapes are reconstructed by sinusoid subcomponents. (c) The peak-to-peak (PTP) amplitudes of the spikes are measured and the spatial location of the single neuronal field is estimated by two different functions: (d) the peak position of the interpolated field and (e) the center of field. (f) The projections of these two functions are clustered by using a K-means clustering algorithm and visualized in a 2-dimensional projection of a 3-dimensional coordinate system where the y coordinate represents the "center of field" or the "interpolated peak" relative to the electrode sites (1 to 4) and the x coordinate represents the average amplitude. Color scale indicates the firing rate of neurons. (g) The resulting clusters of spikes are separated. (h) Auto- and cross-correlation matrix is created to test the refractoriness and unit independence, respectively. (i) Clusters are recombined and reclustered based on the refractory test.

 

Center of field: Analogous to the term of 'center of mass', the 'center of field' is estimatedated by the mean of the weighted amplitudes. First, peak-to-peak amplitudes are calculated for each channel and stored along with the times of their occurrence. The amplitude of the event at each recording site is weighed by a factor determined by the interelectrode distance and the order of the recording site (e. g., 1 to 16) as the first moment. The mean of weighted amplitudes are then plotted as a function of the sum of the amplitudes (Fig. 2.13). The xy coordinates were given by the functions:

(1)

and

, (2)

 

 

where n is the number of channels and is the distance of the ith electrode site (i. e., the order of recording sites). is the amplitude of the j event at the ith channel. The factomes">factor designates a spatial momentum for each simultaneously measured amplitudes. The estimated source is necessarily located within the range of the electrode sites. Note, that the center of field provides only one dimensional determination of the source parallel to the electrode axis.

Interpolated field position: Since electrical events propagate passively in the extracellular space, their amplitude correlates inversely with the distance of the source from the electrode. With multiple recording sites, the source of the event can be estimated by using interpolation. Assuming that the field potential changes nonlinearly in the extracellular space, a cubic-spline interpolation of the measured amplitudes recorded at each site is used. Interpolation of the simultaneously registered amplitude values (y) allows to locate the real amplitude peak between electrode sites (Fig. 2.13). The position of this peak (z )on a continuous scale is assumed to reflect the relative location of the field source. I use sample values where refers to the location of the jth recording site. The peak position is defined as:

  (3)

at a point where

. (4)

The interpolation of y is based on the amplitude at the discrete points:

 , where (5)

and

 , ,

, . (6)

The cubic spline interpolation (5-6) is taking into account of the first and second derivatives of a given point in order to provide a polynomial function which is smooth in the first derivative, and continuous in the second derivative (Press et al., 1992). Since the first and last channels last channels have to be included when the derivatives of the first and last points are calculated, I appended two additional channels as channel 0 and channel n+1 with 0 amplitude of signal. The position of the amplitude peak relative to the electrode sites provides an estimate for the location of electrical source. Plots of peak positions are expected to form clusters.

Spontaneous field events were recorded simultaneously at 16 sites along the CA1-dentate gyrus axis. The recording sites were spaced at 100 µm. The 16-channel amplitude vectors and "the center of field" were calculated for each successively identified field event. The distribution of the detected events was grouped by K-means clustering where K (the number of clusters) was varied. The K at which F was maximal was considered the be the optimal partitioning. The "center of field" versus amplitude plots revealed three well-separated clusters (Fig. 2.14). The amplitude variance of the sharp waves was almost three-fold that of DS1 and more than six fold that of DS2. sharp waves formed a clear cluster between sites 2 and 4 on the virtually continuous scale of the multisite electrode (virtual axis from 1 to 16) and without an overlap with DS1 or DS2. The estimated field generators of DS1 and DS2 were located between 10 and 13 on the virtual axis and were much closer to each other than to sharp waves. Yet, clustering of multiplple-site recorded data clearly separated DS1 and DS2 events. Classification was significantly improved when the cluster of sharp waves was removed from the data base. The clustering method positively identified each sharp wave, 92% of DS1 and 68% of DS2 detected by visual inspection of each event.

 

Spatial Localization of Electrical Sources: Extracellular Units

Having established our ability to reliably detect field events by "spatial" methods, I used a similar approach for unit-cell separation. Since parts of the method are similar to spike separation developed for "wire-tetrode electrodes", only the differences are emphasized here. These differences take advantage of the linear arrangement of the recordings sites of silicon probes.

The first step is the conversion of simultaneous recorded spike events into a spatial domain. Briefly, spike events are plotted in a 3-dimensional space using the "center of field", the "interpolated field position" measures and amplitude as x, y and z coordinates (Figs. 13 and 15). The second step attempts to separate the events (units) into functionally meaningful clusters (Fig. 2.15).

Fig. 2.14. Spatial clustering of intermittent EEG events. (a) Simultaneous recording of field activity (16 recording sites; 100 µm tip intervals) in the CA1-dentate axis of the dorsal hippocampus during awake immobility. For clarity, only every second trace is displayed. Filled arrows indicate sharp wave (SPW) in the CA1 region and type 1 and type 2 dentate spikes (DS1 and DS2). Open arrow in trace 4 indicates SPW-associated high frequency (200 Hz) field oscillation ("ripple") in the CA1 pyramidal layer. Trace 14 is the granule cell layer. (b) Amplitude vs. estimated spatial position plot of sharp waves (SPW) and dentate spikes (DS1 and DS2). The abscissa indicates the peak amplitudes of the EEG events and the ordinate corresponds to the spatial location relative to the electrode sites. The distributions of estimated sources of dentate spikes (DS1 and DS2) are well clustered and perfectly separated from the sharp waves. Note the large amplitude overlap among each classes of events, in contrast to their stable spatial clustering. (c) Cumulative histograms of the events as a function of recording sites. The distributions of DS1 and DS2 differed significantly (t= 14.98, P=0.00).

 

 

 

Fig. 2.15. Three aspects of the spatial projection of the same set of clusters. The three coordinates are: the center of field, peak position, and the sum of amplitudes. Each color represents different clusters. (a) The K-means clustering resulted in eight clusters including clusters with noise and ambiguous distribution. Since clusters with ambiguous distribution can hide other clusters, it is critical to rotate and selectively remove clusters for better observation. (b) The main clusters can be better revealed by the removal of the noisy and fuzzy clusters.

 

Clustering and its Problems

In general, clustering is the grouping of points based on various mathematical criteria. K-means clustering splits the points by hyperplanes (n-1 dimensional planes of the n dimensional Cartesian space) or spheres into a selected number of non-overlapping groups. The algorithm is maximizing between-cluster variances relative to within-cluster variances or using Euclidean point-to-point distances (Hartigan, 1975; Hartigan and Wong, 1979). Unfortunately, we can not use the within-cluster variances or Euclidean distances for predicting the quality of lity of data prior clustering since they depend on the cluster centers and the number of clusters. The quality of data depends mainly on the dispersion of points, therefore I introduced a measurement to assess the degree of dispersion. Based on simulations, I found that the standard average distance of the points (), as an analog to the coefficient of variation, can be used as a measure of dispersion independent from the clustering:

(7)

If the average of the point-to-point distances is low relative to the standard deviation of the total number of distances, the standard average distance, , will be small. For a sufficiently small the partitioning results in separate Gaussian distributions of points in at least one dimension. In contrast, if is large, the Gaussian clouds will be overlapping in each dimension (Fig. 2.17b). Consequently, the partitioning will necessarily be ambiguous. If the original projections are overlapping, cluster separation e. g., by K-means clustering, will nec necessarily result in false identification of spikes with overlapping parameters (arrows in Fig. 2.16). In such ambiguous data sets, typical of multiple unit data, complementary strategies should be applied (see Post-hoc Tests and Reclustering). In our experience, the reliability of unit separation depends more on the projection functions than on the sophistication level of the clustering method used. If the local densities of different clusters overlap considerably, their partitioning becomes difficult. In such cases, it is safest to delete heavily overlapping clusters from the data set.

 

Fig. 2.16. The problem of overlapping clusters. (a) True type clustering of two actual neurons is illustrated by open and filled circles on an amplitude-peak position plot. The two clusters are outlined by two overlapping dotted ellipsoids. Each ellipsoid represents the proposed cluster border for that neuron. The overlapping area includes spike positions that were identified as originating from neuron 1 (E symbols) and spikes which originated from neuron 2 (J symbols). Three spikes generated by neuron 1 in the overlapping area are indicated by arrows. (b) The same amplitude - peak position plot, clustered byred by K-means clustering. Dotted lines indicate hyperplanes which separate the clusters from each other. The K-means clustering divided the clouds into three partitions. These clusters are apparently different from the true type clusters. Arrows indicate falsely grouped spikes by K-means clustering. Since K-means clusters are partitioned on the basis of maximal between-cluster variances relative to within-cluster variances or Euclidean distances, this type of error is highly probable when clusters are overlapping.

 

Another problem associated with clustering is the cluster anisotropy. If cluster shapes are elongated and closer to each other than the internal variance of the clusters, K-means clustering algorithms may fail to split points between the visually recognizable clusters. One solution to overcome such failures is the linear transformation of the data along the dimension of overlapping distributions that compresses the elongated clusters so that it makes them more distinct. Another solution is to overestimate the number of clusters and recombine them subsequently on the basis of post-hoc tests, such as cross-correlations. Alternatively, one can apply hierarchical clustering by recursive bisectioning of the initial set of points and let the clusters aggregate based on the maximal autocorrelation (Fee et.al.,1l.,1996). In many cases it is effective to predetermine visually observed clusters as areas or centers just like the "seed cases" and pre-partition the data. Then, the K-means clustering can aggregate rest of the points to these seed cases.

Clustering may also be achieved by neural-networks by representing distance vectors as connection weights. The network is then trained to provide the best fit to the cluster requirements. At the final cycle of weight modifications, the distance vectors are assigned to clusters on the basis of minimum weights. Several algorithms provide unsupervised clustering (e. g., Kohonen, 1984; Ylinen et al., 1995).

 

Post-Hoc Tests and Reclustering

Spike clustering alone is not always sufficient for identification of single neurons. As discussed previously, omission errors and false identification of neurons is inherent in all present methods. Verification of single units is often possible by application of simple post-hoc tests based on the refractory properties of neurons. Following a single action potential, the neuron remains silent for at least the duration of the Na+ spike itself and spike after-hyperpolarization. The earliest time a neuron may emit the next action potential coincides with the onset of spike afpike after-depolarization. The magnitude and duration of spike after-hyperpolarization is determined not only by the neuron type, but is also determined by the state of the neuron. For example, hippocampal pyramidal cells can fire at 100-300 Hz during a complex-spike burst, although their typical frequency does not exceed 50 Hz in the absence of complex-spike bursts. Not all neuron types are ideal for refractory tests. Some neurons may discharge up to 1,000 Hz (Buzsáki et al., 1983; Steriade et al, 1993; Gray and McCormick, 1996), making refractory tests less useful.

On the basis of the above reasoning, autocorrelograms of unit discharges with clear-cut refractory periods provide a reliable measure about distinctness of clusters and the lack of falsely identified units within clusters. Conversely, a clear refractory period in the cross-correlogram of separate clusters is an indication that the clusters in question reflect activity of the same neuron. Such clusters should therefore be combined, unless independent measures can verify that one of the clusters corresponds to an inhibitory interneuron. Conversely, lack of a significant refractory period in the autocorrelogram is an indication for reclustering (Fig. 2.13). The reliability of recursive reclustering may be improved significantly by removing unambiguously identified clusters from the data base (Fig. 2.15).

Large-scale recordings of unit activity may result in an exponential increase of the pairwise cross-correlograms. However, post-hoc correlation tests should be carried out only from unit clusters recorded by the same probe, since laterally placed electrodes are unlikely to record from the same cells (see above).

 

Effect of Sampling Frequency and Spike Reconstruction

How does the sampling rate influence the quality of unit separation? Since the critical parameter of unit descriptors is peak-to-peak amplitude, precise identification of spike peaks is essential. If the peak of the extracellularly recorded action potential falls between consecutive sampling points, the uncertainty of peak detection will introduce a substantial source of variation (aliasing). As Fig. 2.17 indicates, sampling rate below 10 kHz progressively increases aliasing errors, resulting in the emergence of spurious clusters.

I also examined whether reconstruction of spike shapes would compensate for the aliasing error associated with low frequency sampling rate. Each spike shape can be represented as a combination of sinus waves. Eight sinus components were sufficient to model various spike shapes. A fast Fourier transformatisformation was carried out on each unit samples. The first 8 components of the power- and phase-spectra were extracted and the waves hape was reconstructed by an inverse Fourier transform. The Fourier spike reconstruction "improved" the sampling rate by a factor of ten (the original 24 points samples were substituted by 240 points). A comparison of unit separation with and without spike reconstruction is shown in Fig. 2.17. The results indicate that Fourier reconstruction of unit waveforms did not significantly improve the reliability of spike recognition. This result, however, does not imply that other spike reconstruction methods (e. g., spline) may not improve the precision of peak detection.

Fig. 2.17. Effect of sampling rate on the cluster dispersion. (a) Comparison of cluster dispersion for reconstructed and non-reconstructed spike waves at different sampling rates. The dispersion index is an estimate for cluster separability -- the smaller the better the expected cluster separation. The best cluster separability can be achieved for both reconstructed and non-reconstructed spike waves by recording at a 20 kHz sampling rate. Fourier reconstruction of spike forms did not provide additional benefit. (b) The calculation of thef the dispersion index is based on the average normalized Euclidean-distances of the location space plot. The upper panel illustrates that when the distribution of four points in metric space are more dispersed (box 1), the average point-to-point distance, as represented by is larger than for a more condensed distribution (box 2). The bottom panels shows the projection plot of non-reconstructed spikes extracted from the same recording by sampling at 2.5 kHz (left) and 20 kHz (right) rate. The difference in the indexes predicts the cluster separability. c. Examples of 16 superimposed spikes extracted from the same recording at different frequencies illustrate the effect of sampling rate and Fourier reconstruction on the spike shape.

 

 

 

EXPERIMENTAL PROCEDURES

 

Surgery. Five male rats of the Sprague-Dawley strain (400-900 g) were used. They were anesthetized with a mixture (4 ml/kg) of ketamine (25 mg/ml), xylazine (1.3 mg/ml) and acepromazine (0.25 mg/ml) and placed in the stereotaxic apparatus. Both wire electrodes (7 rats) and silicon electrode arrays (2 animals) were used for recording of neuronal activity, as described previously (Csicsvari et al., 1998). Briefly, wire "tetroe "tetrodes" were attached to a multidrive array and 4 tetrodes were independently moved during the experiment. The three shanks of the silicon tetrodes (Ylinen et al., 1995) were moved simultaneously. Two 50 µm single tungsten wires (with 2 mm of the insulation removed) inserted into the cerebellum and served as ground and reference electrodes.

Recording and data processing. Several days after the surgery, the electrodes were slowly moved from the cortex into the hippocampus. Instrumentation amplifier dyes, mounted on the head of the animal, were used to reduce cable movement artifacts. Electrical activity was recorded during sleep while the rat was in its home cage (session 1) followed by exploration in the home cage (session 2). Three rats were trained to run in a wheel for a water reward (Buzsáki et al., 1983). For these animals, session 2 contained running and drinking behaviors, followed by a final recording period during subsequent sleep (session 3). After amplification (5,000-10,000X and band-pass filtering (1 Hz-5kHz; Model 12-64 channels; Grass Instruments, Quincy, MA), field potentials and extracellular action potentials were recorded continuously using parallel-connected PC486 computers with ISC-16 analog-to-digital converter boards (12-bit resolution; RC Electronics, Santa Barbara, CA) or a 32-channel DATAMAX system (16-bit resolution; RC Electronics). Thehe data were digitized at 10 or 20 kHz. Recording sessions lasted from 10 min to 20 min. After each recording session, the data were transferred for spike detection and sorting to an 133-MHz Pentium personal computer running under LINUX operating system and stored on 4-mm DAT tapes.

Spike sorting. Details of the spike sorting procedure have been described (Csicsvari et al., 1998; Nadasdy et al., 1998). Briefly, spike waveforms were separated on the basis of their spike amplitude and waveform. The information encoded in the amplitude values were compressed using principal component analysis (PCA). Typically, the first 3 principal components were calculated for each channel. Therefore, a single spike was represented by 12 waveform parameters as a 12-dimensional feature vector. Units were identified and isolated by a graphical clustering method (Wilson and McNaughton, 1994; Skaggs et al., 1996). Only units with clear bounderies and >2 msec refractory periods are included in the present analysis (Fig. 2.18 a,b and c).

 

METHODS OF SPIKE SEQUENCE DETECTION

Periods of hippocampal theta oscillation during the wheel running task, exploration and REM sleep were detected by calculating the ratio of the theta (5-10 Hz) and delta (2-4 Hz) fr Hz) frequency band in 2.0 sec windows. A Hamming window was used during the power spectrum calculations. Intervals where the theta-delta power ratio was at least 3:1 were considered to be periods of theta activity. The exact beginning and end of theta epochs were manually adjusted. Next, the individual theta waves were identified. The wide-band signal was digitally filtered in the 5-28 Hz range. The negative peaks of the theta waves were detected because the positive peaks of the theta waves are less prominent in the pyramidal layer. The intervals between successive negative peaks served as reference time points for normalizing theta cycle duration. The individual spike trains were considered as point processes. I refer to the data base of neuronal spike times of several neurons in a given rat as the "parallel spike train". For the detection of invariant temporal structures of spikes from parallel spike trains, two different methods were used: (1) a template matching method and (2) congruency map method. The statistical significance of sequences detected by the template matching method, was tested by Monte Carlo statistics. The statistical significance of sequences, detected by the joint probability map method was tested by Fisher’s exact probability test. The convergence of these two independent methods was also investigated.

The template matching method. The template m matching method was a modified version of the "sliding-sweeps" algorithm introduced by Gerstein et al. (Dayhoff and Gerstein, 1983a; Abeles and Gerstein, 1988; Frostig et al., 1990a). Similar to the "sliding sweeps" algorithm, the template matching method was designed to search for repeating patterns in parallel spike trains. The search for repeating spike sequences was carried out within a specific time window, denoted as the template window, w (Fig. 2.18d). Complex-spike bursts of pyramidal cells (i. e., spikes with <6 msec interspike intervals; Ranck, 1973) were regarded as single events represented by the 1st spike.

Fig. 2.18. Method of spike sequence extraction. (a) Multiunit activity was recorded simultaneously from multiple tetrodes. Filtered recordings from a single tetrode are shown. (b) Spikes were detected and spike shapes were extracted from the filtered recording. (c) Spike sorting based on PCA or/and spatial clustering method resulted in 4-8 neurons/electrode. The validity of clustering was confirmed by refractory tests (Csicsvari et al., 1998; Nadasdy et al., 1988). (d) Spikes (vertical tics) were represented by their time of occurrence. The The spike times of the simultaneously recorded neurons (cells 0 to 4) constitute a "parallel spike train". The parallel spike train was analyzed by a sequence-search algorithm for detecting repeating spike sequences. All possible sequences were considered as a template. The duration of the template window (w) varied from 100 to 400 msec. The tolerance for a perfect match was 10 or 20 msec (spike window; D t). Recurrence of the template spike configuration was registered as a repetition. Mismatch events were rejected but used as templates in subsequent searches. Spike sequences were represented as vectors (e) and repeating spike sequences were superimposed. The significance of sequence repetition was tested by (f) Monte Carlo statistics and (h) Fisher’s exact probability test. For the Monte Carlo statistics random spike trains were generated by shuffling the spikes in the original spike trains in various ways (see Methods). (g) Another approach for searching repeating spike sequences used the joint probability map (JPM) method. The distribution of spike triplets (a, b and c) within the w time window was investigated by constructing a joint peri-event time histogram. The JPM was derived from the joint peri-event time histogram by subtracting chance combinations, as predicted from the corresponding spike doublets. The pixels of tthe difference-map (JPM) represents the excessive number of triplets. (h) The significance of spike triplet repetitions was tested by Fisher’s exact probability test.

 

The algorithm of sequence detection was the following: The 0 point of a w time window was positioned to a spike of a pre-selected neuron (reference neuron) and denoted as the reference spike. The temporal positions of c number of successive spikes within the time window w were considered as a template. These positions were represented by a c i,0 vector of intervals between the t0 reference spike and the c-1 co-occurring spikes from the other spike trains, as

c i,0 = {t0a , c t1a , c t2a , .. , c tca } and c tnj <= w

where a={1,..,N} is the index of the cell from the N parallel-recorded cells and w is the template window. For the sake of simplicity, a sequence is denoted as (c1,c2,c3;t1,t2) (Abeles, 1993). For example, (3,4,1; 125,180) den; 125,180) denotes a spike triplet where the first spike is generated by neuron #3 (time zero), followed by a second spike by neuron #4 at 125 msec and a third spike by neuron#1 at 180 msec. Next, the template was shifted to successive spikes of the reference neuron throughout the recording session and recurrences of the c i, template were counted. During the search, each spike configuration which occurred within the w time window relative to a reference spike was considered as an exemplar e j,0 ={t0, e t1, e t2, .., e tn}and compared to the c i,0 template sequence. A constant maximum spike time window dT (or spike "jitter") was allowed for a match (Fig. 2.18d). Since all mismatch exemplars were regarded as templates, all sequences in a predetermined time window were identified. After the whole parallel spike train was searched, spikes of another neuron served as the reference neuron and the search continued until all possible spike sequences were revealed. In short, the entire parallel-recorded spike train was exhaustively searched for rmin recurrences of c complexity spike sequences within a w sequence window with a dT precision. After determining the number of "above chove chance" occurrence of the repeating spike sequences (see below), the sequences were visualized as temporal vectors (Fig. 2.18e). The different spikes sequences were color-coded and superimposed.

The dependent variables of the sequence search were the number of different sequences (m), and the number of repeating spike sequences (r). The m and r are orthogonal variables since a sequence detection can result in all combinations of number of different sequences and average repetition. For a given c number of successive spikes (complexity), the relationship between m and r was expressed by plotting the number of different sequences against the average of the number of times they repeat (Fig. 2.18f). The number of different sequences (m) was typically an exponential function of the number of sequence repetitions (r). In an ideal spike train where each spike is detected to be a part of a repeating sequence, the product of the average repetition and the number of sequences would be a constant, hence the m=f(r) function is linear.

Testing the significance of repeating spike sequences by using Monte Carlo statistics. The significance of the incidence of recurring spike sequences, detected by the template matching method, was tested by comparing the real spike tre trains with their randomized versions (surrogates). I assumed that in a parallel spike train with randomly occurring spikes but with the same first order statistics (firing rate and spike frequency distribution) as in the original spike train, the number of repeating spike sequences should reflect chance occurrences. Spike shuffling thus served to disintegrate the "inter-spike train" dependency and to eliminate the temporal correlation. Four types of randomization procedures were applied: across-spike train spike shuffling, within-spike train ISI shuffling, within-spike train spike displacement (Fig. 2.19) and within-spike train theta phase-invariant spike shuffling.

Fig. 2.19. Simulation of independent spike trains by shuffling the position of spikes in the original parallel spike train (a) in different ways. A short epoch of the original parallel spike train of five neurons is schematically illustrated here. Three repetitions of the same (1,2,3,4) spike sequence are represented by tics. A trace of the ongoing field oscillation is represented by the sinusoid at the top. (b) Elimination of temporal correlation between the spikes of different cells is accomplishelished by shuffling the inter-spike intervals (ISIs) within each spike train . Grey tics, original spikes. For example, the a,b,c sequence of intervals in the original spike train of neuron#4 is converted to b,c,a intervals. This shuffling method preserves the firing rate of an individual cell but may reduce its field-related modulation. (c) Elimination of temporal correlation between the spikes of different cells by spike displacement. Spikes of the original spike train (gray tics) were randomly shifted in time by 0 to 50 msec (D t; black tics). Although the interspike intervals may somewhat change by this method, the field-modulation of the neuron is better preserved. (d) Elimination of temporal correlation between the spikes of different cells by shuffling spike times between neurons. For example, spike occurrences a and d in the original spike train (gray tics) are displaced to another spike train (black tics). This method preserves population modulation of the neurons but may reduce firing rate differences, which may be present in the original spike train. A fourth method ("phase invariant spike shuffling") is illustrated in Figure 3.5.

  1. Across-train shuffling is a shuffling method that preserves the general temporal relationship among the parallel spike trains. In s. In this method, spikes are exchanged between randomly selected spike trains (Fig. 2.19d). As a result, the population level modulation of the firing rate in the surrogate spike trains remains the same as in the original spike train. A potential caveat of this procedure is that the differences in discharge frequencies of individual spike trains, which may be present in the original spike trains, are reduced as a result of spike shuffling across trains.

(2) The within-spike train shuffling was used to randomize the temporal structure of the spike trains without altering the interspike interval histogram and firing rate of the cell. First, interspike intervals were derived from the original spike trains and numbered from 1 to n (Fig. 2.19a). Second, the intervals were exchanged between two pseudo-randomly selected positions from 1 to n (Fig. 2.19b). Third, this procedure was iterated a number of times. Forth, the spike trains were recreated using the randomized spike times. Within-spike train shuffling preserves average firing rates of individual cells. However, it can eliminate population synchrony among the simultaneously recorded spike trains, present during theta and sharp-wave patterns.

  1. A modified version of within-spike train displacement was also used ino used in order to preserve population synchrony across the parallel-recorded neurons. In this method, spike times were displaced by adding a random interval from —25 to 25 msec. This range was small enough to preserve population synchrony both during theta waves and sharp-waves, which are at least twice as long in duration (Fig. 2.19c). On the other hand, the within train spike displacement method permitted the determination of the optimal spike window dT, i.e., how much the spikes should be shifted in time to reduce the number of repeating spike sequences to chance level.

(4) A phase-invariant shuffling method was introduced in order to preserve the periodic modulation of discharge frequency within and across the spike trains more precisely (shown in Fig. 3.5). This method could be used only for spike trains obtained during wheel-running sessions in which regular rhythmic theta waves were present continuously. First, the peaks of the field theta waves were identified. Second, the spike times were converted to phases of the theta cycle. This way the momentary variation in theta wave duration could be eliminated. Third, the phase-encoded spikes within a given theta cycle were exchanged with other pseudo-randomly selected cycles within the same spike train. The procedure was carried out independently for each spike train, thus the precise timing of spikesikes between original parallel spike trains was altered. However, the periodic modulation of the firing rate within and across spike trains remained the same as in the original recording.

Shuffling of the original spike trains may not eliminate all non-random effects and the spike dynamics in successively shuffled surrogate trains may not be identical. To minimize the variability, shuffling of the original parallel spike trains was carried out 100 times. I reasoned that if the number of sequence repetitions in all of the 100 simulated spike trains is smaller consistently than the number of repetitions obtained from the original spike train, the null hypothesis can be rejected with p<0.01 confidence (Fig. 2.18f).

For comparing different shuffling methods I used an 11 min long parallel spike train during which a continuous theta activity was observed in association with wheel running behavior. This spike train was shuffled in three different ways: within-train ISI shuffling, across-train shuffling and phase-invariant shuffling. Each shuffling method was applied one hundred times, resulting in 300 surrogate spike trains with more or less temporal structures preserved (Fig. 2.20). Both the repetition curves and the probability distributions of repetitions consistently show that the across-train shuffling results in the largesargest number of repeating sequences (r). Phase-invariant shuffling results in a slightly less average repetition and the within-train ISI shuffling eliminates the most. The large number of repetitions preserved by the across-train shuffling implies that most repetitions can be occurred due to an overlapping activity of the cells (during theta and sharp waves). Within-train shuffling methods reduces the temporal overlaps.

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Fig. 2.20. Comparison of different shuffling methods. (a) Repetition curves of spike trains generated by within-train ISI shuffling, across-train shuffling and phase-invariant shuffling. One hundred surrogate parallel spike trains were generated by each method. (b) The probability distributions of the repetitions for the same three shuffling methods as in (a). Error bars are the SDs.

Joint probability map method. For the investigation of the temporal distribution of repeating spike triplets within the w time window, congruent spike triplets were detected by the joint peri-event time histogram methodam method (JPTH). The design of JPTH is analogous to the joint peri-stimulus time histogram (Aertsen et al., 1989) with two modifications: (1) the cross-correlation matrix of two spike trains was triggered by spikes of a third neuron and (2) spike 1 had to follow spike 2. The construction of JPTH was restricted to spike triplets co-occurring within a w time window regardless of the specific temporal position of the spikes within a sequence. First, all possible n!/(n-3)! combinations of temporal orders of triplets were determined, where n is the number of parallel spike trains.

D i,0 = {t0a, D t1a, D t2} where Dt1 < Dt2 and D t2 <= w.

All triplets (neuron1,neuron2,neuron3; D t1, D t2) with D t1<D t2 and w ³ D t2 were registered and represented as points in a two-dimensional coordinate system with D t1a and D t2 coordinates as x and y, respectively. Torespectively. To better visualize the distribution of superimposed spike triplets, the w time window was subdivided into b intervals (bins) and triplets co-detected at the same temporal positions were binned together. For the estimation of the chance occurrences of triplets, the cross-product of the (neuron1| neuron2), (neuron1| neuron3) and the (neuron2|neuron3) cross-correlograms were constructed and normalized in such a way that the total number of expected and observed triplets was the same but their distribution might be different (Fig. 2.18g). This histogram represented the temporal distribution of the expected triplets. Next, the histogram of expected triplets was subtracted from the histogram of observed triplets, resulting in a histogram of unexpected triplets (joint probability map, JPM). The significant occurrences of triplets above the calculated values from the doublet occurrences were calculated by the Fisher's exact probability test for each pixel.

Testing the significance of JPM by Fisher's exact probability test. The chance probability of a spike triplet was assessed from the product of the probabilities of spike doublets. I reasoned that if the observed probability of the triplet was significantly higher than the probability of random combinations of spike doublets, the difference may deririve from non-random processes. Each pixel of the JPM was tested with the Fisher’s exact probability test (Fig. 2.18h). The logic for testing the probability of observing spike triplet abc at the D t1, D t2 position is as follows. The configurations of (), (), (), () spikes are detected with N(), N(), N(), N() frequency, respectively. Our null-hypothesis is based on the assumption that (ab) and (ac) sequences are independent, therefore the probability of joint () occurrences is a product of the probabilities of individual (ab ) and (ac ) events:

H0: P() = P(ab) *P(ac)

If the triplets are not random processes in our database then the alternative hypotheses must be true:

H0: P() > P(ab) *P(ac)

If P() is significantly larger than the product of P(ab) and P(ac), it implies that spike triplets are not generated randomly. In order to calculate P(ab) and P(ac), and test H0, a contingency table of the possible spike configurations was created. For a sequence of abc spikes the number of N(), N(), N() and N() spike configurations were contrasted against each other (Fig. 2.18h). Using Fisher's exact probability test, one can estimate the exact probability of detecting N() as independent processes of N(ab) and N(ac) spike sequences (Frostig, 1990a). To minimize type-I error which may increased when considering large number of pixels, the calculated probability of a triplet was multiplied by the number of pixels of the JPM. This procedure was performed on the shuffled surrogate trains as well and incidence of significant pixels in the JPM of the original and shuffled trains were compared.

Computation. The sequence search, spikspike train shuffling and the Monte Carlo statistics were running on an IBM SP2 scalable parallel computer with 6 nodes of RS/6000, 120MHz P2SC processors (IBM, Inc., White Plains, New York), on a Silicon Graphics Onix2 with a 120MHz MIPS R10000 processor (Silicon Graphics, Inc., Mountain View, California) and on a Sun Enterprise with two UltraSPARC processors (Sun Microsystems, Inc., Palo Alto, California). Identification of repeating spike sequences in a 10-min long file, containing 5 parallel spike trains, and its shuffled surrogates typically required average 35 min on Onix2, 50 min on Sun and 2.5 hours on SP2 (single node). The complete hypothesis testing of a parallel spike train of one rat, including the generation of 100 surrogates and sequence search at 30 levels of repetition, required 35x101x30 ~ 106 min (=1767 hr, ~73 days) on the Onix2.

HISTOLOGICAL PROCEDURES

Following completion of the experiments the rats were deeply anesthetized and perfused through the heart first with cacodylate-buffered saline (pH 7.5) followed by a cacodylate-buffered fixative containing 4 % paraformaldehyde and 5.9 % calcium chloride (pH 7.5). Brains were left in situ for 24 hours, removed and then postfixed in the same solution for one week. The brains were sectioned by a Vibratome at 100 µm in t in the coronal plane. The sections were stained with the Gallyas silver method (Gallyas et al., 1992).

 

 

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