Cognitive and Computational Neuroscience at UCSC

Welcome to the Samaha Lab

Our lab uses psychophysics and computational modeling in concert with tools from cognitive neuroscience to measure and manipulate the human brain.  We seek to understand the neural basis of visual consciousness, attention, perceptual decision making, metacognition, and working memory, and have a particular interest in the role of neural oscillations in these domains. 

We are housed within the Department of Psychology at the University of California, Santa Cruz. 

Subject Sammy


entry: 5.12.24

Wei Dou's new paper showing that EEG signals that reflect evidence accumulation dynamics uniquely predict perceptual confidence ratings is now out in Psychological Science

While making perceptual decisions, people often feel a sense of confidence in their choice. This metacognitive capacity is critical for making adaptive behaviors, such as learning from mistakes or optimizing the allocation of limited cognitive resources. In this research, we investigated how the brain computes confidence by recording electroencephalograms (EEGs) while participants were performing motion-perception tasks and rating confidence. We found a neural signal around 300 ms after viewing the motion stimulus and 250 ms prior to making a decision that indexed participants’ confidence regardless of their decision accuracy, response time (RT), and the evidence quality of the stimulus. Our findings indicate that confidence computation in the brain is more complex than just evaluating whether the decision is right or wrong, how quickly people make decisions, and how good the evidence contained in a given stimulus is.

Neural signatures of evidence accumulation encode subjective perceptual confidence independent of performanceW Dou, LJ Martinez-Arango, OG Castaneda, L Arellano, E. McIntyre, C Yballa, J Samaha Psychological Science
entry: 3.31.24

April Pilipenko's new paper gets featured in the Journal of Neuroscience! We show how alpha waves and pupil fluctuations independently shape vision

We found that synchronous brain waves in the alpha-band (around 10 Hz) lead to inhibited visual perception regardless of the stimulus intensity level, even during stimulus absent conditions. This type of "additive" mechanism implies that alpha waves may boost or inhibit visual detection regardless of whether there is a stimulus, leading to false percepts (or hallucinations). Simultaneously, changes in people's pupil size, which reflect arousal levels, revealed a boost in perception for strong but not weak stimuli, suggesting that high arousal leads to more accurate perception (with fewer false percepts). Thus, alpha waves and pupil-linked arousal have different effects on perception, but both contribute to variability in our experience of the same stimulus. Congrats to April on publishing your first-year project!

Double dissociation of spontaneous alpha-band activity and pupil-linked arousal on additive and multiplicative perceptual gainA Pilipenko, J Samaha Journal of Neuroscience [OA LINK]
entry: 3.1.24

Special Focus in the Journal of Cognitive Neuroscience: Alpha-band dynamics and temporal processing.

Huge thanks to all the contributors who wrestled with the question of if and how alpha-band oscillations relate to temporal processing. The contributions span new empirical work, meta-analyses, and opinion pieces motivated, in part, by recent null findings in our field. Into to the Special Focus here: 

Alpha-band Brain Dynamics and Temporal Processing: An Introduction to the Special Focus

J Samaha, V Romei Journal of Cognitive Neuroscience

entry: 9.8.23

New pre-print on how alpha oscillations and pupil fluctuations jointly shape visual detection and confidence

Double dissociation of spontaneous alpha-band activity and pupil-linked arousal on additive and multiplicative perceptual gainA Pilipenko, J Samaha biorXiv

In a project led by PhD student April Pilipenko, we found that states of weak ongoing alpha oscillations lead to a boost in visual detection and confidence that was independent of stimulus strength. In other words, spontaneous alpha amplitude  fluctuations exerted additive gain on perception, boosting detection reports even for absent stimuli and increasing confidence for strong stimuli and decreasing confidence for weak stimuli. Conversely, pupil-fluctuations occurring contemporaneously with alpha changes exerted  multiplicative gain on stimulus detection and confidence. Large pupil states (thought to reflect high arousal) boosted confidence and detection more for strong than weak stimuli. Importantly, pupil-independent fluctuations in alpha were still found to induce an overall additive factor to detection, suggesting that alpha and pupil-linked arousal have dissociable influences on perception and that alpha activity alters perception via an additive shift in excitability that is independent of stimulus strength. 

entry: 9.8.23

Three new lab publications

Evaluating the evidence for the functional inhibition account of alpha-band oscillations during preparatory attentionA Morrow, M Elias, J Samaha Journal of Cognitive Neuroscience

PhD Student Audrey Morrow led a project reviewing evidence for the 'functional inhibition' theory of alpha oscillations by summarizing the literature linking attention modulation of pre-stimulus alpha power and attention modulation of subsequent stimulus-evoked brain responses. Audrey's review finds that most studies that examine attention-related changes in alpha do not correlate those changes with attention effects on stimulus-evoked responses, and those that do find mixed evidence for whether pre-stimulus alpha modulations predict changes in sensory- of decision-related brain responses.

Brain signatures indexing variation in internal processing during perceptual decision-makingJ Nakuci, J Samaha, D Rahnev iScience

In a collaboration with researchers at Georgia Tech, led by postdoc Johan Nakuci, we discovered two distinct sub-types of brain activity that participants switch between during perceptual decision making. These two sub-types reflect different decision strategies corresponding to changes in thresholds required to terminate sensory evidence accumulation.

Task feedback suggests a post-perceptual component to serial dependence JM Fulvio, B Rokers, J Samaha Journal of Vision

This project investigated the impact of feedback on serial dependence (the finding that perceptual reports are biased towards recently seen stimuli). We found that providing feedback virtually abolishes serial dependence in a 3D motion perception task. This implies that serial dependence may be partly post-perceptual since simply telling subjects if they were correct or not is not expected to rapidly shape perception.

entry: 2.5.23

New paper shedding doubt on the idea that alpha frequency modulates the latency of early visual processing

PhD students Audrey Morrow and Wei Dou analyzed data from 42 participants who underwent visual stimulation using stimuli designed to produce "C1" ERP components (electrical activity thought to index afferent visual cortex responses). They correlated the latency of each participants C1 with their individual alpha frequency to test the hypothesis that individuals with faster alpha frequencies have earlier visual cortex activation. Using several different methods of quantfying C1 latency, they found virtually no correlation between the two, suggesting that, although alpha activity may reduce the amplitude of sensory responses, alpha frequency does not seem to modulate their latency.

The paper appears in a special issue in Frontiers in Neuroscience alongside other great papers investigating peak oscillation frequencies.

Individual alpha frequency appears unrelated to the latency of early visual responses

A Morrow*, W Dou*, J Samaha Frontiers in Neuroscience *these authors contributed equally 
entry: 2.5.23

Lab eats (and presents) at the Cognitive Neuroscience Society (CNS) meeting!

Check out some of the ongoing work we shared in poster form!

Individual Alpha Frequency Appears Unrelated to the Latency of Early Visual Responses. A Morrow, W Dou, J Samaha
Non-conscious Multi-sensory Integration Revealed in the Ventriloquist EffectE Turkovich, S Sankaran, W Dou, J Samaha 
Effects of Spontaneous Alpha-band Activity on Visual DetectionAcross the Perceptual Contrast Response FunctionA Pilipenko, S Afrakhteh, A Feghhi, A Gergen, N Gupta, J Samaha
Metacognitive Introspection Modulates Evidence Accumulationfor Decision MakingW Dou, S Afrakhteh, K Callwood, A Feghhi, J Samaha
Does spatial attention operate rhythmically?No evidence for behavioral Θ oscillations in criterion or sensitivityJ Samaha
entry: 2.10.23

New paper on the influence of expectations on serial dependence.

MCD biology PhD student Stefan Abreo helped lead a project investigating how our recent perceptual experience influences current perception and how this is impacted by expectations. We found that in the absence of expectations, people report stimuli as being more similar to the past than they really were. However, when stimuli were expected they were reported as being further away from the past than they really were. When stimuli violated expectations they were once again reported as being more similar to the past. This shows that expectations can reverse serial dependence from an attractive to a repulsive bias and that serial biases do not depend on continuity in the environment - explicitly violating expectations can still produce strong serial effects.

Effects of Satisfying and Violating Expectations on Serial DependenceS Abreo, A Gergen, N Gupta, J Samaha Journal of Vision
entry: 10.7.22

New PhD student April joins lab + several new pre-prints!

Welcome to April Pilipenko, who joined the lab this fall as a PhD student! April's first project is examining how ocular data and alpha jointly predict perception. 

We also have a few new pre-prints out related to metacognition and serial dependence! See links below. 

Unique Effects of Sedatives, Dissociatives, Psychedelics, Stimulants, and Cannabinoids on Episodic Memory: A Review and Reanalysis of Acute Drug Effects on RecollectionM Doss, J Samaha, FS Barrett, R Griffiths, H de Wit, D Gallo, J Koen biorXiv
Task feedback suggests a post-perceptual locus of serial dependence JM Fulvio, B Rokers, J Samaha biorXiv
Behavioral and neural measures of confidence using a novel auditory pitch identification taskT Tang, J Samaha, MAK Peters PsyArXiv
entry: 5.4.22

New paper replicates and extends the finding that prestimulus alpha power biases subjective visibility, not accuracy

Numerous papers have now shown that the amplitude of ongoing alpha oscillations prior to stimulus onset biases confidence, visibility, and detection criterion, but not discrimination accuracy or d'. We extend these findings by replicating the effect but in the domain of high-level perceptual judgments.  That is, even for decisions about more complex stimuli (faces versus houses) stronger prestimulus alpha oscillations reduced subjcetive visibility judgments, without change objective discrimination accuracy. Open access link below!

Spontaneous alpha-band amplitude predicts subjective visibility but not discrimination accuracy during high-level perception

J Samaha, JJ LaRocque, BR Postle Consciousness and Cognition
entry: 3.15.22

New paper published showing that the phase of pre-stimulus alpha activity modulates early visual cortex responses 

A project spearheaded by PhD student Wei Dou shows that incoming visual signals are modulated by the phase of ongoing alpha oscillations en route to primary visual cortex. By measuring C1 activity (an early ERP component thought to arise from excitatory input to primary visual cortex), Wei showed that alpha phase, particularly when strong in amplitude, impacts early visual activity. This finding sheds light on the neurophysiological origin of alpha phase effects on perception by suggesting that feedforward activity is phasically gated by alpha oscillations at the level of primary visual cortex or before. 

Pre-Stimulus Alpha-Band Phase Gates Early Visual Cortex Responses

W Dou, A Morrow, L Iemi, J Samaha Neuroimage
entry: 1.25.22

Methods paper on 1/f activity and instantaneous frequency now published

Using simulated and real EEG data we show that the "slope" (or 1/f-like activity) of the power spectrum can bias the results of instantaneous frequency analyses. In the presence of steep 1/f slopes, changes in oscillation amplitude alone can bias frequency estimates.  We provide a method for correcting the bias. If you use the frequency sliding method or other instantaneous frequency measures based on narrowband filtering, you might wanna check it out. 

Power spectrum slope confounds estimation of instantaneous oscillatory frequency

J Samaha, MX Cohen Neuroimage
entry: 6.28.21

New paper published in EjN and a new methods paper pre-print on 1/f activity and instantaneous frequency.

Audrey Morrow's project looking at individual differences in the flash-lag and Fröhlich illusions has now been published in the European Journal of Neuroscience special issue on "Rhythms in Cognition". Her experiment found no correlation between the flash-lag and Fröhlich illusions across subjects, which indicates that they do not depend on the exact same mechanism of discrete sampling at a constant frequency. The special issue has many great papers ( Congrats Audrey!

We also have a new pre-print up with Mike X Cohen using simulated spectral data to show how the slope (or 1/f-like activity) of the power spectrum can bias the results of instantaneous frequency analyses.  If you use the frequency sliding method or other instantaneous frequency measures based on narrowband filtering, you might wanna check it out. 

No evidence for a single oscillator underlying discrete visual percepts

A Morrow, J Samaha European Journal of Neuroscience

Power spectrum slope confounds estimation of instantaneous oscillatory frequency

J Samaha, MX Cohen biorXiv
entry: 4.14.21

Two new lab pre-prints on neural oscillations and sensory brain activity

In "Pre-Stimulus Alpha-Band Phase Gates Afferent Visual Cortex Responses" led by lab Ph.D. student Wei Dou, we find that the phase of ongoing alpha-band oscillations modulated the afferent cortical response to a visual stimulus, as captured by EEG responses taken during the time window of the C1 event-related potential component. We take this as evidence for a thalamic inhibition model of alpha, consistent with animal models of alpha that posit generators of phasic inhibition in the LGN.

In "Spontaneous neural oscillations influence behavior and sensory representations by suppressing neuronal excitability" collaborator Luca Iemi and colleagues analyzed electrocorticography data recorded across many brain areas to ask how oscillatory amplitude modulates broad-band gamma activity in response to visual and auditory stimuli. We report that alpha and beta power inversely correlates with spontaneous and stimulus-evoked broad-band gamma activity - an effect that mediated reaction times in a discrimination task. Interestingly, a pattern classifier trained to discriminate different stimuli found that ongoing alpha power modulated the magnitude of the responses, leading to higher classifier confidence, but no change in classifier accuracy.

Pre-stimulus alpha-band phase gates afferent visual cortex responses

W Dou, A Morrow, L Iemi, J Samaha biorXiv

Spontaneous neural oscillations influence behavior and sensory representations by suppressing neuronal excitability

L Iemi, L Gwilliams, J Samaha, R Auksztulewicz, YM Cycowicz, JR King, VV Nikulin, T Thesen, W Doyle, O Devinsky, CE Schroeder, L Melloni, S Haegens biorXiv
entry: 1.6.21

New pre-print suggests that a unified visual sampling rate does not explain both the Flash-lag and Fröhlich effect.

In this project led by Ph.D. student Audrey Morrow, we find that individual differences in the magnitude of two motion illusions - the flash-lag and Fröhlich effect - are not correlated. Prior theory has suggested that the two illusions are driven by discrete sampling in the visual system, which has been suggested to occur at the rate of the alpha-band oscillations. However, the finding that these two illusions are not correlated indicates that they are produced by different mechanisms. Whereas discrete sampling may still be correct, this null effect suggests that different oscillation frequencies could underlie the illusions or that oscillations are not the neural implementation of discrete sampling at all. Alternatively, discrete sampling may not drive these illusions and alternative accounts, for example, based on motion extrapolation and masking may explain the flash-lag and Fröhlich effect, respectively. 

No evidence for a single oscillator underlying discrete visual percepts

A Morrow, J Samaha biorXiv
entry: 8.6.20

Pre-registered report on reconstructing working memory representations under different states of prioritization

Led by Quan Wan in the Postle lab, we show, across two experiments (one pre-registered) that a stimulus held in working memory (WM) but in an unprioritized state (e.g., when attending to a different working memory item) is represented in a pattern of neural activity that is "inverted" compared to when that same item is prioritized. This suggests that unprioritized WM items are maintained in active patterns of neural activity, as opposed to being 'silent',  but in a qualitatively distinct neural code, as opposed to simply being weaker. Great work by Quan and team!

 Open access link below!

Tracking stimulus representation across a 2-back visual working memory task. Quan Wan, Ying Cai, Jason Samaha and Bradley R. Postle. Royal Society Open Science

entry: 7.9.20

New paper on the role of PFC in perceptual metacognition

There is growing debate around the role of the prefrontal cortex (PFC) in sensory metacognition. In this paper, lead by UCSB prof. Regina Lapate, we add new evidence in support of a causal role of PFC to human metacognition by perturbing the dorsal-lateral PFC with MRI-guided transcranial magnetic stimulation (TMS). TMS to dlPFC was specifically found to impair metacognitive awareness (the extent to which subjective visibility ratings discriminate between task performance) without changing task performance. This was all done in the context of a face discrimination task, thereby extending prior results into the domain of higher-level perception of socially-relevant stimuli. Open access link below!

Perceptual metacognition of human faces is causally supported by function of the lateral prefrontal cortex

RC Lapate, J Samaha, B Rokers, BR Postle, RJ Davidson Communications Biology
entry: 6.7.20

New TiCS review on neural oscillations and perceptual decision-making

We reviewed decades of evidence linking spontaneous fluctuations in the amplitude of low-frequency neural oscillations as well as more recent experiments using signal detection theory frameworks. We suggest that weak prestimulus alpha amplitude enhances early sensory responses, which causes sensory activity to surpass detection and confidence/visibility criteria more frequently. However, the global nature of such spontaneous excitability fluctuations means that sensory activity reflecting all decision options are equally enhanced so that discriminability (or d') is unchanged, leading to a dissociation between subjective awareness (detection, visibility/confidence) and objective performance (accuracy/sensitivity). Special thanks to co-authors Luca Iemi, Saskia Haegens, and Niko Busch!

link to pdf of paper

entry: 3.17.20

New preprint: The positive evidence bias in perceptual confidence is not post-decisional

We investigated at what stage of processing the "positive evidence bias" (PEB) in human confidence occurs. We find that the bias is not explained by post-decisional mechanisms (e.g., by assuming that additional evidence accumulates after the perceptual decision is made). This suggest the PEB emerges in perception itself or during the decision process.

biorXiv link / data and code

entry: 12.11.19

"Confidence Database" paper accepted in Nature Human Behavior

We are thrilled to be part of a new resource for the community working on confidence and decision making. As part of a multi-site initiative led by Doby Rahnev, a new paper describing a database of confidence experiments with over 8,700 participants has just been accepted at Nature Human Behavior. We contributed some of our datasets on perceptual estimation and confidence in perception and short-term memory. 

Data and code are here (

Pre-print is here (

The database is still accepting experiments. Consider contributing!

entry: 9.2.19

STEM Diversity Poster Session

Undergraduate researchers Lleymi Martinez (right) and Olenka Graham Castaneda (left) present their work in the lab looking at neural correlates of subjective confidence in motion perception. We used a novel paradigm that controls for objective accuracy in motion direction discrimination but leads to changes in subjective confidence. Under these conditions, it seems like late components of the event-related potential - which have previously been associated with confidence under non-performance matched conditions - still tracks subjective reports of confidence!

2019 UCSC STEM Diversity poster faire

entry: 7.10.19

New Paper in eLife!

Iemi et al find that prestimulus neural oscillations have opposite effects on the early and late visual-evoked response. We found suppression of the C1 and N1 ERP component by prestimulus alpha- and beta-band power, as predicted by functional inhibition theories of low-frequency oscillations. Interestingly, however, the same prestimulus oscillations led to enhanced late (>200 ms) ERP components, which we can explain by a baseline shift mechanism (caused by modulation of oscillations with non-zero mean). We hope this paper adds to the discussion about the functional role of alpha/beta oscillations and the neural generators of ERPs!

entry: 4.3.19

Chin/headrests are expensive! We made a step-by-step guide on how to make your own research-quality headrest for visual psychophysics for about $100 using computer monitor stands and some wood! [PDF]

entry: 2.10.19

Register now! The Northern California Consciousness Conference @ UC Davis March 15th: