Adaptive Hierarchical Encoding in Model Neurons and H1

Erik Flister, Emily Anderson

June 2006



We propose a novel experiment design to investigate stimulus encoding and adaptation in sensory neurons.  Neurons are exposed to repeated trials of a nearly identical time-varying stimulus.  The stimulus is divided into three sections, the first and third of which never vary.  The first stimulus section serves to reset the neuron into an identical adaptive state across trials.  The stimulus is modified systematically for the middle section of each trial, revealing how small stimulus changes are reflected in the spike timing of the neural response.  Due to differential adaptation during this middle section, responses to the identical final section vary, reflecting their context-dependence.  Our stimulus design exposes the decaying time dynamics of this memory effect.  We demonstrate the design in model neurons and the motion-sensitive H1 fly neuron, revealing adaptation to stimulus variance ("contrast") in both cases.  Our key novel theoretical contributions are 1) that features are encoded by spike "swoops" that respect temporal boundaries between features, 2) that this pattern holds for sub-features within features, forming a fractal pattern so that encoding is hierarchical, 3) that spike times within a single trial correspond to stimulus features at varying, rather than consistent, latency, 4) that refractory effects serve to delay, rather than prevent, future spikes, and 5) refractory effects play an important role in very short-term adaptation.



            Spike times in sensory neurons across phylogeny, from the periphery to high-order cortices, have proven to encode dynamic stimuli that contain suitably high frequencies with reliability and precision (Mainen and Sejnowski).  The classic experiment that demonstrates this is to repeat the same stimulus over many trials while recording the spike times of the neural response.  The peri-stimulus time histogram (PSTH) describes the observed probability of spiking at each time following stimulus onset across the trials, and typically comprises discrete "events" during which the neuron fires at most once; this property is known as "sparse" encoding.  Measures of the event widths (typically the variances of fitted Gaussians) indicate the temporal precision of spike times, while their integral indicates the event reliability, the probability that any given response will spike during the event.

            Sensory neurons are also frequently found to adapt, which means that their encoding scheme is context sensitive, so that they encode identical stimuli differently depending on the recent stimulus history.  Adaptation may have the teleological purpose of improving efficiency, the number of spikes required to encode a fixed amount of information about the stimulus.  Sensory neurons often respond only to changes in stimuli, which avoids costs associated with using spikes to encode static stimuli.  This could be compared to a common form of video compression designed for efficient transmission of "talking head" scenes that involve very little motion; since frame-to-frame differences are small, it is more efficient to assume a static scene and only represent violations of this assumption than to represent time-varying luminance directly.  This is one form of adaptation, since the same absolute stimulus may evoke a large response if it is different from preceding stimuli, while evoking only a baseline response when there is no change.  Adaptation of this kind could be explained as a non-adaptive response that simply encodes the time-derivative of the stimulus, rather than the stimulus itself.

            Another form of adaptation is a tuning of the response to maximize dynamic range, given the range of values recently occupied by the stimulus.  Contrast adaptation in the visual system is an example of this; stimulus encoding is relatively insensitive to contrast.  That is, when luminances have been within a small range for a while (low contrast), visual neurons adjust so that they encode contrast-independent scene information (edge locations, for example) in about the same way as when luminances vary across a wider range (high contrast).  For a short time after contrast suddenly changes, neurons will encode the same stimulus differently (at lower efficiency, less information per spike), because they have not yet had time to adapt to the new contrast regime and adjust their dynamic range to match the signal content (Denning and Reinagel).

            Reverse correlation techniques are often used to more or less accurately recover the function that describes how sensory neurons encode stimuli in spike times (first- (spike-triggered averaging) and second-order (spike-triggered covariance) Wiener-kernel methods, Bialek).  This approach is often successful for recovering the encoding function over small time scales, and usually reveals the differentiating-filter (high-pass) properties of sensory neurons.  But stimulus dimensionality over the long time scales associated with other forms of adaptation is often too large to allow adequate sampling.  Moreover, most reverse correlation techniques (all except "maximally informative dimensions" (Sharpee)) only work for Gaussian stimuli; since natural stimuli are not typically Gaussian, such techniques are limited to studying neural response to stimuli with unnatural 3rd- and higher-order moments (spectral frequency content, the second moment, can be matched to that of natural stimuli, but higher order moments are uniquely constrained by the first two moments for Gaussian processes).  Thus, slow adaptation dynamics, especially in the natural stimulus regimes that sensory neurons are presumably phylo- and ontogenetically optimized to represent, are not easily probed.


Figure 1.  Example raster plots demonstrate spike time precision and reliability.  These data were recorded by Erik Flister in Pam Reinagel's lab.  They are from an LGN neuron recorded via a chronic tetrode microdrive implant in an awake behaving rat.  The stimulus was time-varying full-field luminance.  In one case (B), the stimulus was Gaussian and contained no temporal correlations ("white"), while in another (A), it was drawn from a single pixel of a monochromatic movie shot at human eye-level while walking through a forest during daylight (van Hateren).  Raster plots separate trials vertically and show spike times as dots, positioned horizontally according to when they occurred relative to the stimulus.  Also shown (C) is the spike-triggered average stimulus (the average stimulus that preceded a spike in the white dataset), which represents the best single linear filter approximation of the cell's stimulus-to-spike transfer function.


Experimental Design

            We designed a novel experimental paradigm to reveal qualitative features of spike time encoding and adaptation.  Real and model neurons are presented with repeated trials of identical noise stimuli, using a waveform produced by some stochastic process.  During a middle section of the stimulus, a parameter is varied by small amounts across trials, but the stimulus is identical for the first and final sections.  The first section serves to replicate the results discussed above; the responses to these identical stimuli should be reliable and precise across trials and demonstrate the stationarity of the neuron's behavior.  This section also serves to equalize the neuron's adaptive state; it should be longer than the neuron's memory, so that by the end the neuron always responds the same way.  During the middle section, the original waveform is modified by small steps in some systematic way.  The neural response should demonstrate how the neuron encodes small changes in the varied parameter when it is in the adaptive state induced by the first section of the stimulus.  During the final section, the stimulus is again identical across trials.  If the neuron were in a constant adaptive state during this section, its response would be reliable and precise, as it was in the first section.  However, to the extent that the parameter variations in the middle section change the adaptive state of the neuron, its response to the final section will show context dependence.  As the neuron "forgets" about the middle section of stimulus, this context dependence will disappear, so the variations in response to the last section should reveal the time dynamics of adaptation.

            Here it is important to point out that, in the case of in vivo recording, we are recording from a single neuron whose activity is a measure of the activity of the whole neural network presynaptic to it; thus its "memory" may be much longer than is possible for a single neuron in isolation.

            The parameter we vary is the noise variance (also called amplitude or contrast).  We achieve this by simply multiplying the middle section of the waveform by a constant.  We slowly vary the magnitude of this constant from negative to positive values across trials (ideally the values would be shuffled over trials so that the results will not be confounded by non-stationarities such as subtle electrode drift or diminishing health of the preparation, although we did not shuffle here).  Many other parameters could be gradually varied instead:  the waveform could be shifted, expanded or compressed in time, its mean could be shifted, it could be filtered for frequency content, or sections could be silenced, to give just a few examples we are interested in.  For the model neurons, the stimulus was injected current.  For H1, a motion sensitive neuron in the early fly visual system, the stimulus was the horizontal position or velocity of a spatially varying luminosity pattern.  But in principle any physical quantity within the receptive field of a sensory neuron could be driven in this way:  full field luminance (vision), vibration (somatosensation), sound-pressure level (audition), and so on.  In order to probe H1 as closely as possible to its natural operating regime, our spatial pattern consisted of Gaussian noise filtered to enjoy a "natural" 1/f spectrum, as did our velocity and position profiles, and current injection in the case of the model.



Figure 2.  Stimulus.  Our example stimulus is 1/f Gaussian noise, divided into three sections.  The first and final section (A, C) are always identical across trials.  The middle section (B) is multiplied by a constant that slowly varies from a negative to a positive value over trials, thus altering the stimulus variance (equivalently, "amplitude" or "contrast") during that section and reversing the waveform polarity.  These waveforms are used to drive current injected into model cells or the position or velocity of a spatial pattern for H1 (D).



            The model cells we used were the Izhikevich model (Izhikevich), an extremely efficient 2-dimensional dynamical model with 4 parameters that allows very close quantitative approximation to the physiological behavior of a wide variety of known cell types.  Given the intriguing nature of the results, it would be interesting to check the response of simpler models, including integrate-and-fire, quadratic-integrate-and-fire, and inhomogeneous Poisson and gamma point-processes with rate governed by a thresholded linear filter (linear-nonlinear-Poisson (LNP) and -gamma LNG models).  Much of the dynamical model response appears to involve refractory-like effects, which will not be captured by any of these simpler models except LNG, and positive feedback, not captured by any except quadratic-integrate-and-fire.  We would also like to test map-based models, which do capture positive feedback and refractoriness (Timofeev).

            The key observation in the model response is the hierarchical reverse-J structure.  This stimulus paradigm allows, for the first time, the identification of single spike events that correspond to the same feature across trials, even though the spike itself occurs at widely disparate times.  As features in the stimulus waveform become large enough to be resolved by the neuron (cross threshold), they first cause spikes with high latency -- it has long been known that low-contrast stimuli are processed with higher latency by sensory neurons.  As the feature becomes larger, it causes a faster depolarization, which causes the positive feedback chain-reaction of sodium-channel activation that underlies a spike to occur with lower latency.  Thus, the spike time asymptotes quickly from its initial high latency to a fixed, short latency with respect to the feature.  We will refer to the resulting single-spike reverse-J structure across trials as a "swoop."  Then, as additional details of the feature become resolved, more spikes follow the same pattern, swooping in behind the original spike.  A key point revealed here is that, in any one trial, individual spikes are occurring with dramatically different latencies.  This insight, presented here for the first time, flies in the face of typical reverse-correlation analyses, which explicitly assume that each spike encodes stimulus information at a consistent relative time-lag. 

            A second key point, also novel, is the hierarchical nature of the encoding.  As features grow in strength, additional spikes swoop in behind the initial ones, occurring first with high latency and then with low latency, joining together to form low-latency bursts that represent the features.  Intriguingly, temporal (vertical) boundaries between features are respected -- "swoops" from adjacent features never overlap.  This pattern holds for sub-features within features, resulting in a hierarchical fractal-like pattern.

            Refractory effects played an important role in the response, particularly when a weak feature was followed by a stronger feature.  Since the strong feature becomes resolved first, some of its spikes are established by the time the weaker feature's spikes appear.  When they do, their refractory effect delays, but never prevents, the subsequent features' spikes.  This effect seems to preferentially affect spikes that have not yet asymptoted; well-established low-latency spikes are not perturbed, but the effect can actually jump over them to affect subsequent nascent spikes.  This refractory effect appears to play the majority role in adaptation effects for this single-neuron model.

            Prior to seeing the model response, we expected spike bifurcations to play a much larger role.  Bifurcations occur, but are relatively rare.



Figure 3.  Model response reveals variable-latency hierarchical encoding and refractory effects that can delay, but not prevent, subsequent spikes. 

            The horizontal time scale measures half milliseconds.

            A  A single swoop is highlighted. 

            B  Hierarchical secondary-swoops that join together to form a low-latency burst are highlighted. 

            C  Vertical boundaries that separate features are shown.

            D  Refractory effects delay, but do not prevent, subsequent spikes as preceding features become resolved.  This effect is absent for well-established low-latency spikes, and can even transfer to spikes that follow them.

            E  Refractory effects play a role in adaptation.

            F  A rare spike bifurcation.


            For the in vivo H1 experiments, our stimulation equipment did not allow precise temporal control below about 10ms, and likely could not adequately simulate smooth motion, although we were able to prevent the disaster of jitter accumulation (see Methods).  Despite the limitations, our results confirmed the model predictions of asymptoting latency, hierarchical fractal-like encoding, and did exhibit adaptation.  These promising preliminary results encourage a system upgrade to investigate at high precision whether the fine temporal features of our model predictions hold at a precise spike-timing level in vivo. 

            During the variable part of the stimulus, spike events asymptoted from high to low latency and exhibited the same hierarchical swooping behavior as the model.  During the adaptive portion, when the stimulus was identical but context varied, the neural response showed adaptive trends that depended on context.  The most obvious adaptive feature was a large increase in spike rate in response to the same stimulus intensity when it was preceded by lower stimulus intensity.  This was even more apparent at the beginning of trials, which was preceded by an inter-trial interval of around 30s of darkness.


Figure 4.  Physiology.  Extracellular potential was recorded at 20 or 30kHz (blue) from an isolated physiology amplifier configured to pass 300Hz-10kHz at 10,000X, and filtered (red) using an optimal zero-phase 60th-order FIR filter designed by Matlab's fir1() to have a pass-band from 5-99% of the Nyquist frequency.  Spike times (black markers) were identified by upward-going threshold crossings at 3.5 times the standard deviation of the filtered signal (black).  Note that this spike detection algorithm turned out to be terrible; it catches multiple threshold crossings per spike, so the threshold should be much higher and single-sided.


Figure 5.  H1 position response. 

            100 trials.  An entire trial contains 3000 frames and lasts a little less than 60s.  The zero-motion trial was around trial 30.

            A  Spatial pattern position varied across trials.

            B  Spike rate response is shown in pseudo-color, lightly smoothed with a 2-D Gaussian filter.  The top 2% of rates, which corresponded to artifacts from episodes of fly motion, are clipped, to improve dynamic range.  Non-stationarity across the experiment is clearly visible; the cell became better isolated and responded more strongly to the beginning of trials as the experiment progressed.

            C  Raster of actual spike times.

            D  Detail on variable period shows spike events asymptoting in different directions and hierarchical fractal swooping.

            E  Detail of transition from variable to adaptive portions of response.  Approximate location of transition (*).  During the adaptation period, increased response to identical stimuli when preceded by low-velocity stimuli is visible.  This is also visible in B as the high rates that follow the ~30s inter-trial dark interval.


            When the stimulus parameter is velocity, the stimulus waveform must be integrated to recover position.  Since the initial position was always the same, the middle section of varying velocity causes the positions to diverge from trial to trial, so that in the final section, pattern velocity is conserved but stimuli are not identical because position is offset.  H1 response reflected positional offset, probably because the offset moved features used for motion estimation into and out of its receptive field.  A better future design for investigating adaptation would be to offset the positions at the beginning of the trials so that the varying velocity section will cause them to exactly align for the final section.  It is not possible to merely reverse the velocity waveforms because time-reversal does not conserve the phase spectrum.



Figure 6.  H1 velocity response.

            100 trials.  An entire trial contains 3000 frames and lasts a little less than 60s.  The zero-motion trial was around trial 30.

            A  Spatial pattern velocity varied across trials according to a waveform similar to that in 2A.  When driving pattern velocity, the stimulus waveform must be integrated to recover position.  Since the initial position is always the same, the middle section of varying velocity causes the positions to diverge from trial to trial, so that in the final section, pattern velocity is conserved but stimuli are not identical because position is offset. 

            B  Spike rate response as in 5B. 

            C  Raster.  The cell was lost for the final few trials (*).  Spontaneous activity in the dark can be seen during the beginning of the inter-trial interval (o).  H1 response reflected positional offset, probably because the offset moved features used for motion estimation into and out of its receptive field.


            E  Detail of transition from variable to adaptive portions of response.  Approximate location of transition (*).  Dark streaks are fly motion artifacts.

            F  Detail of the adaptive portion of response.  Tracking of position offset is clearly visible as chevrons.



            Female flies (the male fly visual system is more designed for pursuit of small dark objects against a bright background, and does not give good full-field motion response) were dissected as previously described (Tumer) and placed near the center of an arena surrounded by 96 columns of LEDs, which spanned 3 degrees of horizontal visual field each.  A 96-channel digital I/O National Instruments card, the PC-DIO-96, tells each column of LEDs whether it should be set to a high or low luminance, while an analog card sets the actual value for the high and low luminances.

            Evren Tumer wrote a LabView program ("/Seth Brundle/") that can present rotating patterns described by two luminance values.  Unfortunately, he found that the 3 degrees spanned by the LEDs were within the spatial resolution of the fly visual system, so that H1 responds as if it is seeing the individual discrete jumps as the pattern moves across LEDs, rather than smooth motion (the neural response is simply a burst of spikes each time the pattern moves by one LED).  His software also does not allow the arbitrary definition of stimulus waveforms, as required by our experimental design.  He has another LabView program ("/Seth Brundle/"), that does allow arbitrary definition of time-varying full-field luminance, but it did not produce the expected results when we tried it.  Therefore, we decided to write our own stimulus presentation software, but is convenient for locating and isolating H1.

            To overcome the resolution problem, we do not restrict the spatial pattern to two luminance values, but discretize an arbitrary waveform into n luminance values (n=10 for our experiments).  Because higher n reduces the presence of hard edges in the stimulus and prevents boundaries between luminance values from shifting on the same "frame," this approach provides a closer approximation to smooth motion for a fixed spatial resolution.  The values are gamma-corrected and each frame in the stimulus is created by interlacing n "sub-frames," each of which lights up the appropriate LEDs at its gamma-corrected luminance value.  This has two deleterious effects.  It reduces temporal resolution by a factor of n, and since each LED is on for only one of n sub-frames, overall luminance and contrast are drastically reduced.  A future improvement would be to choose the n luminance values dynamically, optimally distributing them to the values actually requested frame-by-frame, rather than statically allocating them uniformly over the full range of possible values.  We did not have time to assess whether the waveform discritization approach created an adequate approximation to smooth motion; the data we recorded could be analyzed to reveal whether bursts of spikes merely followed frame or sub-frame transitions.  The results were subjectively smoother than the 2-luminance value approach, but close examination of a spike raster reveals regularly spaced bursts of spikes, suggesting that the motion is still too coarse.  But this could also be an artifact of the poor spike-detection algorithm that is triggered by multiple threshold crossings per actual spike.


Figure 7.  Regularly spaced bursts of spikes suggest the discretized stimulus is not encoded the same way that continuous motion would be, but this may be an artifact of multiple spike-detections per actual spike.


            We first tried using Matlab's Data Acquisition toolbox, which provides commands for controlling the National Instruments cards that drive the LEDs.  We found that execution timing in Matlab, even when compiled into a function rather than interpreted in a script file, is too slow and variable for our high frequency and precision requirements (minimum line execution time is ~10ms).  We then tried using Matlab's loadlibrary()/calllib() commands to access the c API for the cards directly ("traditional NI-DAQ," available on the National Instruments website at  The hope was that we could access buffering functions on the card not available via the Data Acquisition toolbox.  This would allow the card, rather than Matlab, to control output timing, but it turned out that only 64 of the 96 digital channels on our PC-DIO-96 can be buffered.  So we finally moved to writing in c directly.  Even in c, the call to set a group of 8 channel values (DIG_Out_Prt()) takes on the order of 1ms to return.  In order to maximize temporal resolution, we tried letting c execute as fast as possible, but found that it was semi-periodically interrupted by Windows.  Since accumulating jitter errors in our frame times is disastrous for our experiment, we used the high-precision performance clock available in "windows.h" (QueryPerformanceCounter()), which we believe provides access to the CPU clock.  At the beginning of each trial, regularly spaced frame times were specified for each frame.  If execution arrived at a frame prior to its scheduled time, the clock was accessed in a tight loop until the scheduled time.  If execution arrived late, output was generated as fast as possible until execution caught back up to schedule.  Execution was still variable, but this variability was minimized by "processor hogging" -- setting the process priority to "realtime" (using the DOS command "start /realtime ./stim.exe"), while avoiding running other processes or attempting to distract the computer with keyboard, mouse, or network activity.  In particular, this rendered physiology recording impossible on this computer, so that process needed to be moved to another computer that coordinated with the stimulus computer to record trials.

            To achieve high temporal resolution with this minimum-jitter-accumulation strategy, the requested frame time was reduced until about 1% of frame times were late.  With n=10 luminance values (10 subframes per frame), this corresponded to a frame frequency of about 50Hz, so that each single-luminance subframe was displayed for about 2ms.  Presumably because of remaining Windows interruptions, maximum jitter approached 10ms, which is far too coarse to observe millisecond-precision spike times (neurons can spike more than 5 times in 10ms with jitter <1ms).  Fortunately, the strategy outlined above succeeded in preventing jitter accumulation.  This was the critical requirement for our experiment to be possible at all. 

            Given our promising results, the next step is to upgrade the system to allow very accurate stimulation, so that effects on individual spike times may be observed in order to test the model predictions.  A modern GHz-rated computer will execute the c stimulus program far more quickly.  National instruments has dramatically redesigned the API ("NI-DAQmx," also available on their website) so that it has much better performance, but the modern API is not compatible with our digital card.  The NI-DAQmx library is only compiled for Microsoft Visual C++, so a hack is required to get it to work with other compilers (various options are discussed at  The help files and example c programs included with both traditional NI-DAQ and NI-DAQmx are extremely well written and demonstrate exactly what is necessary for this project (for NI-DAQmx, "Cont Write Dig Port-Ext Clk" is the most relevant example).  The appropriate cards are 2 6224's ($549 each) and a 6229 ($679).  The 6224's have 48 digital channels each, but only 32 can be hardware clocked.  The 6229 will provide the final 32 digital channels, together with the synchronized analog channels necessary to set the luminance levels and record physiology.  This system will allow fast and accurate hardware timing up to 1MHz, which is more than adequate for the purposes described here.  By offloading stimulus control onto the hardware, the system will also allow temporally coordinated physiology recording without the networking complexity and delays associated with our current system.  Matlab's loadlibrary()/calllib() functions should be adequate to access the NI-DAQmx buffering functions, so that c programming and processor hogging will not be necessary.  The final requirement will be an adaptor cable that reorganizes the digital output of the three cards into the same configuration as the current 2x48 channel input to the LED array.

            To use the current system, place "run stim.bat" and "stim.exe" in a directory on the stimulus computer.  Also place a directory called "frames" in this directory.  In "./frames/," define each of your trials in a file called "frames<n>.mat," where <n> is an integer representing the consecutive order of your trials starting with "1."  Each .mat file should contain an m-by-96 ascii-encoded matrix, where each row indicates the desired LED luminance for the mth frame across the 96 LED columns (this value is a real number between 0 and 10).  Edit and recompile "stim.c" to change the value discritization, gamma correction, frame duration, inter-trial interval, or path to the frames folder (in the future, these should really be turned into command line arguments).  "GenFrames.m" (which calls "generateStimFile.m") is a matlab program for automatically generating stimuli of the kind described here.  They provide some advanced functionality -- the number of "missing LEDs" can be set, which enables one to probe whether the fly is sensitive to distortions in the topology of visual space behind her (when a feature disappears off one side of her visual field, does it reappear as expected in the other one?).  Also, a non-linear warping may be defined over the LEDs, which allows further probing of topology integrity questions or simulates the effects of being closer to or farther from visual features (closer objects move faster given equal ego-motion).  "recoverStim.m" is a program for recovering the stimulus waveforms from the generated frame files using cross-correlation to estimate the frame-to-frame positional offset (this is related to the "Reicherdt correlator" theory of motion detection, and algorithmic artifacts -- errors between true and estimated motion -- could help test whether H1 or its inputs are correlation-based motion estimators).

            For best timing, reboot the stimulus computer and don't run any other programs.  Run "run stim.bat" to run the trials, and don't touch the computer during this time (ctrl-c and ctrl-alt-del will eventually interrupt if necessary).  While running trials, the analog card will send trigger pulses on a third analog out channel corresponding to trial beginnings.  Route these triggers to the trigger input on the analog card on the physiology recording computer.  Also route the physiology amplifier to its channel 1 and the high-luminance analog-out channel from the stimulus computer to its channel 2.  Run "acquire.m" in Matlab on this recording computer.  Edit the parameters at the top of acquire.m to change the number of trials, the trial duration, sampling rate, spike-detection filtering/thresholding, etc.  Acquire.m will initiate recordings for a fixed trial duration upon receipt of a trigger from the stimulus computer.  It measures the frame time jitter by looking for the large negative jumps in the high-luminance channel associated with frame boundaries.  It also estimates spike times by zero-phase high-pass filtering (optimal FIR) and variance-based thresholding of the physiology channel, but as discussed in Results, this algorithm is in desperate need of improvement.  After every trial, it will produce a graphical report of the stimulus jitter, spike times, raster-to-date, and so on, but generating this report takes time.  There is no communication back to the stimulus computer, so if the recording computer gets out of sync by taking too long to process, your experiment is hosed.  The code is relatively uncommented and picky, due to time constraints. is happy to help with any questions.



            EA performed the dissections and most fly husbandry.  EF designed the experiment, did the stimulus and analysis programming, most physiology, and wrote this paper.  We thank Evren Tumer for training us on the dissection, Alan White for a requested apparatus modification, and Dan Hill for help with both software and hardware.  We thank David Kleinfeld for access to all of the resources necessary to perform this work.