Biology subjects

Fine, I.

Publications and source records attributed to Fine, I..

17 recordsLinked to original sources

bioRxiv2026

Why phosphenes are not always dots: modeling the shapes elicited 1by intracortical stimulation of human V1

The majority of visual cortical prosthetic devices currently implanted in patients or under development rely on small depth electrodes. Reports from patients implanted with these devices suggest that stimulation with tiny electrodes does not reliably produce small punctate spots, with some patients reporting a variety of percepts, including larger spots and irregularly shaped phosphenes. Here, we compare drawings and descriptions made by a cortical implant recipient to predicted phosphene patterns, generated using a 'virtual patient' simulation based on a simple model of V1. We find that this model successfully reproduces the wide variety of percepts reported by this patient and further suggests that, for a subset of electrodes, stimulation may activate multiple locations -- possibly as a result of axonal activation.

bioengineering↗

bioRxiv2026

"Spilling-in" versus "Filling-in": Disentangling bottom-up drive from predictive completion in human V1 to V3

It is well established that responses in visual areas are a combination of bottom-up stimulus driven input and top-down input driven by expectation. However, it has been difficult to quantify the differential strength of these components, and how they vary across the visual hierarchy. Here, we introduce a method for dissociating bottom-up and top-down contributions in early retinotopic areas (V1-V3). Using a log-scaled bar stimulus, we measured BOLD responses under full-field vs. central scotoma conditions. Using the full-field stimulus, we estimated pRFs in human visual cortex 17 (V1-V3).

neuroscience↗

bioRxiv2026

Blindness reveals that Heschl's gyrus folding is not altered by auditory experience

Heschls gyrus (HG), which contains the primary auditory cortex, shows marked individual variability in its folding pattern, ranging from a single gyrus to partial or complete duplication. Greater HG duplication has been reported in expert musicians, often interpreted as evidence that auditory experience can shape cortical morphology. However, these structural differences might alternatively indicate a bias for musical careers in individuals whose anatomical predispositions facilitate expertise. Here, we examined HG morphology in blind individuals--a population with extensive auditory experience but without selection based on auditory ability. T1-weighted MRI data from 100 human participants (48 females, 42 males, 10 unknown) across blind and sighted groups were analyzed. HG was manually defined in each hemisphere, and folding was measured using both categorical morphology classification and continuous surface-based metrics. Across all analyses, blindness did not increase HG folding. These results suggest that the morphology of HG is largely predetermined. Significance statementIncreased anatomical folding in the auditory cortex has been reported in professional musicians. Is this structural variability due to experience-dependent plasticity, or is it that individuals with increased anatomical folding are more likely to become musicians? We examined Heschls gyrus (HG), which contains the primary auditory cortex, in blind individuals who rely heavily on auditory input. Despite extensive auditory experience, blindness did not alter HG folding. This finding suggests that the morphology of HG is not strongly influenced by auditory experience.

neuroscience↗

bioRxiv2026

Using Virtual Patients to Predict Perceptual Outcomes for Optogenetic Sight Recovery Technologies

Optogenetics is emerging as a powerful approach for partial vision restoration, with at least three ongoing clinical trials in humans testing novel light-sensitive proteins (opsins) in patients with inherited retinal degenerative disorders. These therapies aim to restore light responsiveness by introducing opsins into surviving retinal cells, such as bipolar or ganglion cells, enabling them to generate neural activity in response to visual stimuli. One ongoing difficulty in selecting promising opsins for clinical development is that there is no way to predict patient perceptual outcomes from optogenetically evoked neural activity as measured ex vivo. Here, we introduce a virtual patient framework that quantitatively links the sensitivity and speed of opsin-mediated retinal responses to predicted patient outcomes, and show how this framework can predict temporal contrast sensitivity functions - a well-established measure of perceptual performance - from microbial opsin photocurrent responses. Our simulations demonstrate that opsin sensitivity and kinetics jointly determine perceptual outcomes, and that enhancing sensitivity at the expense of temporal resolution can degrade the perception of fast-moving stimuli. This computational platform provides a generalizable tool for comparing and selecting the most effective opsins for clinical translation, thereby guiding the design and optimization of next-generation sight restoration strategies.

neuroscience↗

bioRxiv2026

COLOR VISION UNDER BLUR: IMPLICATIONS FOR PERCEPTION AND EVOLUTION

Color is a prominent feature of visual experience, yet humans can recognize objects easily and accurately from grayscale images. We examined whether color becomes more useful when spatial information is degraded due to blurring. Participants viewed naturalistic scenes in color or grayscale, and reported whether a named target object was present across a range of blur levels that simulated optical defocus from 0-8 diopters. With unblurred images, performance did not differ between color and grayscale conditions, but as blur increased, recognition accuracy declined. Color provided a modest but reliable advantage at higher levels of blur, suggesting that color becomes increasingly useful when optical quality is degraded. We hypothesize that the evolutionary shift towards trichromacy may have been partially driven by the need to compensate for optical degradation due to aging and/or accumulated light exposure.

neuroscience↗

bioRxiv2025

Enhanced pitch perception in early blind individuals and musicians is due to reduced internal noise

Although it is commonly assumed that early blind individuals have enhanced pitch perception, the literature to date has been contradictory. We measured performance in two tasks known to recruit early vs. late stages of auditory frequency tuning in early blind and sighted individuals with matched levels of musical training. The two groups showed equivalent performance on a tone detection in a notched-noise task that assesses peripheral and subcortical frequency selectivity. In contrast, early blind individuals showed enhanced performance in a pitch discrimination task thought to be mediated by cortical mechanisms. Computational modeling revealed that this enhancement was best explained by reduced internal noise rather than narrower frequency tuning, with both blindness and musical training predicting a reduction in internal noise. These findings identify internal noise as a key factor in experience-driven auditory plasticity as a result of both musical experience and early blindness.

neuroscience↗

bioRxiv2024

Improving the Reliability and Accuracy of Population Receptive Field Measures Using a Logarithmically Warped Stimulus.

The population receptive field method, which measures the region in visual space that elicits a BOLD signal in a voxel in retinotopic cortex, is a powerful tool for investigating the functional organization of human visual cortex with fMRI (Dumoulin & Wandell, 2008). However, recent work has shown that population receptive field (pRF) estimates for early retinotopic visual areas can be biased and unreliable, especially for voxels representing the fovea. Here, we show that a log-bar stimulus that is logarithmically warped along the eccentricity dimension produces more reliable estimates of pRF size and location than the traditional moving bar stimulus. The log-bar stimulus was better able to identify pRFs near the foveal representation, and pRFs were smaller in size, consistent with simulation estimates of receptive field sizes in the fovea.

neuroscience↗

bioRxiv2023

Pulse trains to percepts: A virtual patient describing the perceptual effects of human visual cortical stimulation

The field of cortical sight restoration prostheses is making rapid progress with three clinical trials of visual cortical prostheses underway. However, as yet, we have only limited insight into the perceptual experiences produced by these implants. Here we describe a computational model or virtual patient, based on the neurophysiological architecture of V1, which successfully predicts the perceptual experience of participants across a wide range of previously published cortical stimulation studies describing the location, size, brightness and spatiotemporal shape of electrically induced percepts in humans. Our simulations suggest that, in the foreseeable future the perceptual quality of cortical prosthetic devices is likely to be limited by the neurophysiological organization of visual cortex, rather than engineering constraints.

neuroscience↗

bioRxiv2022

Characterizing amblyopic perception under naturalistic viewing conditions

Current assessments of interocular interactions in amblyopia use rivalrous stimuli, with conflicting stimuli in each eye, which does not reflect vision under typical circumstances. Here we measure interocular interactions in observers with amblyopia, strabismus with equal vision, and controls using a non-rivalrous stimulus. Observers used a joystick to continuously report perceived contrast of dichoptic grating stimuli, identical except that the stimulus was contrast-modulated independently in each eye over time. Consistent with previous studies, a model predicting the time-course of perceived contrast found increased amblyopic eye attenuation, and reduced contrast normalization of the fellow eye by the amblyopic eye, in amblyopic participants compared to controls. However, these suppressive interocular effects were weaker than those found in previous studies, suggesting that rivalrous stimuli may overestimate the effects of amblyopia on interocular interactions during naturalistic viewing conditions.

neuroscience↗

bioRxiv2022

The perception of auditory motion in sighted and early blind individuals

Motion detection is a fundamental property of the visual system that plays an important role across many of the human senses. In vision, motion processing is classically described using a motion energy model which assumes spatiotemporally selective (i.e., non-separable) filters that capture the smooth continuous change in spatial position over time afforded by moving objects. However, in the case of audition, it is still not clear whether or not the primary mechanisms underlying motion sensitivity are spatiotemporally selective. We used a psychophysical reverse correlation paradigm, where participants discriminated the direction of a motion signal in the presence of spatiotemporal noise, to determine whether the filters underlying auditory motion discrimination were spatiotemporally separable or non-separable. We then examined whether these auditory motion filters were altered as a result of early blindness. We found that both sighted and early blind individuals have separable filters. However, early blind individuals show increased sensitivity to auditory motion, with reduced susceptibility to noise, with filters that were more accurate in detecting motion onsets/offsets. An ideal observer model suggested that the reliance on separable filters may be more optimal given the limited spatial resolution in auditory input.

neuroscience↗

bioRxiv2021

Scattering-driven PPG signal model

This article discusses the origin of photoplethysmographic (PPG) signals. Two plausible hypotheses that could explain the phenomenon of pulsatile optical signals are analyzed: the volumetric hypothesis in which changes in the arterial blood volume are responsible for the observed signal pulsation, and a model wherein changes in the measured signal are driven by the size fluctuations of red blood cell (RBC) aggregates. The theoretical approximation where the size of scattering particles representing RBC aggregates varies as a function of pulsatile changes in blood flow is elaborated. Within this models framework, the gamma coefficient used in pulse oximetry was calculated for the volumetric-related and aggregation-related models. Two pairs of wavelengths, (670 nm, 940 nm) and (590 nm, 940 nm), were selected to determine gamma. As a function of aggregate size, the gamma behavior was simulated for these pairs and the two hypotheses. To verify the model predictions experimentally, the PPG signals at the fingertip were measured using reflection geometry. Two combinations of light-emitting diodes with two pairs of wavelengths were utilized as light sources. To manipulate the length of aggregates in the blood, external pressure was applied to the fingertip, presumably reducing the blood flow velocity. The gamma values were determined. The derived results fully agree with the theoretical predictions of the aggregation-driven PPG signal model. In addition, using a pressure sensor, the oscillometric signal amplitude in the fingertip and the PPG signal amplitude were simultaneously measured. The comparison results of oscillometric and optical signals at elevated external pressure values are not consistent with the volumetric hypothesis. All of the foregoing experimental results strongly support the argument favoring the incorporation of the proposed aggregation mechanism into the generic PPG signal model.

bioengineering↗

bioRxiv2020

Assessing Pain in a Noninvasive Manner by Measuring Changes in the Microcirculation

The quantitative determination of the level of pain is one of the most challenging clinical problems. This article proposes a method for quantitative assessment of both acute and chronic levels of pain, based on the analysis of hemodynamic patterns measured using a non-invasive sensor. Hemodynamic characteristics were taken from the finger using a sensor measuring the dynamic scattering of light from the skin surface. Changes in hemodynamic parameters in patients with chronic pain were studied. One group of patients with chronic back pain required epidural injection for pain relief. The second group of patients had a Spinal Cord Stimulator implant which was switched off one hour before arriving at the clinic. Optical signals were collected before and after pain relief, either by epidural injection or by turning on the stimulator. Both groups reported their pain level using a standard numerical rating scale. Processing of the results showed that the changes in measured hemodynamic parameters corresponded in most cases to the changes in pain reported by patients following medical intervention. The results suggest that this new non-invasive measurement of pain can be used both for physiological studies and for monitoring various categories of patients suffering from pain.

biophysics↗

bioRxiv2019

Model-based recommendations for optimal surgical placement of epiretinal implants

A major limitation of current electronic retinal implants is that in addition to stimulating the intended retinal ganglion cells, they also stimulate passing axon fibers, producing perceptual streaks that limit the quality of the generated visual experience. Recent evidence suggests a dependence between the shape of the elicited visual percept and the retinal location of the stimulating electrode. However, this knowledge has yet to be incorporated into the surgical placement of retinal implants. Here we systematically explored the space of possible implant configurations to make recommendations for optimal intraocular positioning of the electrode array. Using a psychophysically validated computational model, we demonstrate that better implant placement has the potential to reduce the spatial extent of axonal activation in existing implant users by up to [~]55 %. Importantly, the best implant location, as inferred from a population of simulated virtual patients, is both surgically feasible and is relatively stable across individuals. This study is a first step towards the use of computer simulations in patient-specific planning of retinal implant surgery.

neuroscience↗

bioRxiv2018

A model of ganglion axon pathways accounts for percepts elicited by retinal implants

Retinal prostheses, now implanted in over 250 patients worldwide, electrically stimulate surviving cells in order to evoke neuronal responses that are interpreted by the brain as visual percepts ( phosphenes). However, instead of seeing focal spots of light, current implant users perceive highly distorted phosphenes that vary in shape both across subjects and electrodes. We characterized these distortions by asking users of the Argus retinal prosthesis system (Second Sight Medical Products) to draw elicited percepts on a touchscreen. We found that phosphene shape could be accurately predicted by simulating the topographic organization of nerve fiber bundles in each subjects retina. Our model shows that activation of ganglion axons contributes to a rich repertoire of phosphene shapes, successfully replicating percepts ranging from blobs to oriented streaks and wedges depending on electrode location. This work provides a first step towards future devices that incorporate stimulation strategies tailored to each individual patients retinal neurophysiology.\n\nOne Sentence SummaryWe show that the perceptual experience of retinal implant users can be accurately predicted using a computational model that simulates the topographic organization of each individual patients retinal ganglion axon pathways.

neuroscience↗

bioRxiv2018

Persistent Underrepresentation of Women’s Science in High Profile Journals

Yiqin Alicia Shen, Jason M. Webster, Yuichi Shoda, and Ione Fine Department of Psychology, University of Washington Past research has demonstrated an under-representation of female editors and reviewers in top scientific journals, but less is known about the representation of women authors within original research articles. We collected research article publication records from 15 high-profile multidisciplinary and neuroscience journals for 2005-2017 and analyzed the representation of women over time, as well as its relationship with journal impact factor. We find that women authors have been persistently underrepresented in high-profile journals. This under-representation has persisted over more than a decade, with glacial improvement over time. Even within our limited group of high profile journals, the percent of female first and last authors is negatively associated with journal impact factor. Since publishing in high-profile journals is a gateway to academic success, this underrepresentation of women may contribute to the lack of women at the top of the academic ladder.

scientific communication and education↗

bioRxiv2017

pulse2percept: A Python-based simulation framework for bionic vision

By 2020 roughly 200 million people worldwide will suffer from photoreceptor diseases such as retinitis pigmentosa and age-related macular degeneration, and a variety of retinal sight restoration technologies are being developed to target these diseases. One technology, analogous to cochlear implants, uses a grid of electrodes to stimulate remaining retinal cells. Two brands of retinal prostheses are currently approved for implantation in patients with late stage photoreceptor disease. Clinical experience with these implants has made it apparent that the vision restored by these devices differs substantially from normal sight. To better understand the outcomes of this technology, we developed pulse2percept, an open-source Python implementation of a computational model that predicts the perceptual experience of retinal prosthesis patients across a wide range of implant configurations. A modular and extensible user interface exposes the different building blocks of the software, making it easy for users to simulate novel implants, stimuli, and retinal models. We hope that this library will contribute substantially to the field of medicine by providing a tool to accelerate the development of visual prostheses.

neuroscience↗

bioRxiv2017

Learning to see again: Biological constraints on cortical plasticity and the implications for sight restoration technologies

1. ABSTRACTThe \"bionic eye\" - so long a dream of the future - is finally becoming a reality with retinal prostheses available to patients in both the US and Europe. However, clinical experience with these implants has made it apparent that the vision provided by these devices differs substantially from normal sight. Consequently, the ability to learn to make use of this abnormal retinal input plays a critical role in whether or not some functional vision is successfully regained. The goal of the present review is to summarize the vast basic science literature on developmental and adult cortical plasticity with an emphasis on how this literature might relate to the field of prosthetic vision. We begin with describing the distortion and information loss likely to be experienced by visual prosthesis users. We then define cortical plasticity and perceptual learning, and describe what is known, and what is unknown, about visual plasticity across the hierarchy of brain regions involved in visual processing, and across different stages of life. We close by discussing what is known about brain plasticity in sight restoration patients and discuss biological mechanisms that might eventually be harnessed to improve visual learning in these patients.

neuroscience↗