Biology subjects

Boynton, G. M.

Publications and source records attributed to Boynton, G. M..

16 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

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↗

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

PySilSub: An open-source Python toolbox for implementing the method of silent substitution in vision and nonvisual photoreception research

The normal human retina contains several classes of photosensitive cell--rods for low-light vision, three cone classes for daylight vision, and intrinsically photosensitive retinal ganglion cells (ipRGCs) expressing melanopsin for non-image-forming functions including pupil control, melatonin suppression and circadian photoentrainment. The spectral sensitivities of the photoreceptors overlap significantly, which means that most lights will stimulate all photoreceptors, to varying degrees. The method of silent substitution is a powerful tool for stimulating individual photoreceptor classes selectively and has found much use in research and clinical settings. The main hardware requirement for silent substitution is a spectrally calibrated light stimulation system with at least as many primaries as there are photoreceptors under consideration. Device settings that will produce lights to selectively stimulate the photoreceptor(s) of interest can be found using a variety of analytic and algorithmic approaches. Here we present PySilSub (https://github.com/PySilentSubstitution/pysilsub), a novel Python package for silent substitution featuring flexible object-oriented support for individual colorimetric observer models (including human and mouse observers), multi-primary stimulation devices, and solving silent substitution problems with linear algebra and constrained numerical optimisation. The toolbox is registered with the Python Package Index and includes example data sets from various multi-primary systems. We hope that PySilSub will facilitate the application of silent substitution in research and clinical settings.

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↗

bioRxiv2020

Divided attention for feature-based selection in visual cortex

Feature-based attention can select relevant features such as colors or directions of motion from the visual field irrespective of the spatial position. In visual cortex not only do we see feature-specific attention affecting responses in neurons with receptive fields at an attended location, but that effect also spreads to neurons with receptive fields beyond the spatially relevant location. When only one feature is task relevant, the spread of activity across space can act to facilitate perception of behaviorally relevant stimuli. However, when multiple features are relevant, what is the effect on behavior and brain activity? We tested this question by having observers divide attention between two patches (left and right of fixation) of moving dot stimuli, each containing overlapping upward and downward motion fields. In one condition, subjects performed a task on motion fields moving in the same direction in both patches. In another condition attention was divided between opposite directions of motion. Replicating a previous behavioral study, we found that observers showed better performance when dividing attention to the same directions of motion than opposing directions of motion. We analyzed the BOLD responses while observers performed this task using an inverted encoding model approach that provides estimates of responses to each of the four component dot fields. We found larger responses to the attended components, replicating previous studies of spatial and feature-based attention. However, these effects were much larger when attention was divided to between the same directions of motion than to opposing directions. Our fMRI results in area hMT+ predict our behavioral results by extending the normalization model of attention to include a global feature-based attention component in that leads to suppressed responses to attended stimulus components when attention is directed to opposing directions of motion.

neuroscience↗

bioRxiv2020

Divided Attention in Perception:A Unified Analysis of Dual-Task Deficits and Congruency Effects

How well can one perceive simultaneous stimuli at two widely spaced visual locations? Are the stimuli processed independently? If not, does the dependency affect perception, disrupt signals in later stages, or both? To address these questions, we measured effects of divided attention using a dual-task paradigm with stimuli presented in noise on either side of fixation. This paradigm was applied to detecting Gabor patches and to the semantic categorization of words. We measured dual-task deficits which are a decline in mean performance for a dual task compared to a single task. There was such a deficit for categorizing two words but relatively little deficit for detecting two Gabors. We also measured congruency effects which are when performance at one location depends on whether the stimulus at the other location requires the same response. There was such a congruency effect for detecting two Gabors but relatively little congruency effect for categorizing two words. Further experiments were consistent with the dual-task deficit in word categorization being perceptual, but the congruency effect in Gabor detection being due to later processes. Results of additional experiments showed that the congruency effect was consistent with either graded selection errors or with all-or-none selection followed by graded interactive processing. To answer our opening question: for Gabor detection, perceptual processes were largely independent but later processes caused congruency effects; for word categorization, perceptual processes had capacity limits but even in combination with later processes caused relatively little congruency effects. In summary, there was evidence for two different kinds of dependency. Such complementary dependencies are inconsistent with theories of divided attention that depend on a single dependency such as a single resource or single source of interactive processing.

neuroscience↗

bioRxiv2020

Set-size effects in change detection depend on failures of retrieval and/or comparison and not on perception, encoding or storage

Set-size effects in change detection is often used to investigate the capacity limits of dividing attention. Such capacity limits have been attributed to a variety of processes including perception, memory encoding, memory storage, memory retrieval, comparison and decision. In this study, we investigated the locus of the effect of increasing set size from 1 to 2. To measure purely attentional effects and not other phenomena such as crowding, a precue was used to manipulate relevant set size and keep the display constant across conditions. The task was to detect a change in the orientation of 1 or 2 Gabor patterns. The locus of the capacity limits was determined by varying when observers were cued to the only stimulus that was relevant. We began by measuring the baseline set-size effect in an initial experiment. In the next experiment, a 100% valid postcue was added to test for an effect of decision. This postcue did not change the set-size effects. In the critical experiments, a 100% valid cue was provided during the retention interval between displays, or only one stimulus was presented in the second display (local recognition). For both of these conditions, there was little or no set-size effect. This pattern of results was found for both hard-to-discriminate stimuli typical of perception experiments and easy-to-discriminate stimuli typical of memory experiments. These results are consistent with capacity limits in memory retrieval, and/or comparison. For these set sizes, the results are not consistent with capacity limits in perception, memory encoding or memory storage. Significance SectionThe change detection paradigm is often used to demonstrate effects of divided attention. But it is not clear whether these effects are due to perception, memory, or judgment and decision. In this article, we present new evidence that the divided attention effect in change detection is due to limits in memory retrieval or comparison processes. These results are not consistent with limits in perception, memory encoding or memory storage.

animal behavior and cognition↗

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↗

bioRxiv2019

Inverted encoding models estimate sensible channel responses for sensible models

In a commentary published in eNeuro, Gardner & Liu (2019) discuss the role of model specification in interpreting the output of complex models of neural data. As a case study, they suggest that one variant of such analyses, the inverted encoding model (IEM) analysis framework, should not be used to assay properties of \"stimulus representations\" because the ability to apply linear transformations at various stages of the analysis procedure renders results arbitrary. As we discuss, the specification of all models is arbitrary to the extent that an experimenter makes choices based on current knowledge of the model system. However, the results derived from any given model, such as the reconstructed channel response profiles obtained from an IEM analysis, are uniquely defined and are arbitrary only in the sense that changes in the model can predictably change results. Moreover, with knowledge of the model used for IEM analyses, the results remain informative as comparisons between reconstructed channel response profiles across task conditions using a fixed encoding model - the most common use of the IEM technique - can generally capture changes in population-level representation magnitude across linear transformations. Thus, changes in the magnitude of the response profiles across conditions are preserved, even across unprincipled linear transforms. IEM-based channel response profiles should therefore not be considered arbitrary when the model is clearly specified and guided by our best understanding of neural population representations in the brain regions being analyzed. Intuitions derived from this case study are important to consider when interpreting results from all model-based analyses, which are similarly contingent upon the specification of the models used.

neuroscience↗

bioRxiv2018

Parallel spatial channels converge at a bottleneck in anterior word-selective cortex

In most environments, the visual system is confronted with many relevant objects simultaneously. That is especially true during reading. However, behavioral data demonstrate that a serial bottleneck prevents recognition of more than one word at a time. We used functional magnetic resonance imaging (fMRI) to investigate how parallel spatial channels of visual processing converge into a serial bottleneck for word recognition. Observers viewed pairs of words presented simultaneously. We found that retinotopic cortex processed the two words in parallel spatial channels, one in each contralateral hemisphere. Responses were higher for attended words than ignored words, but were not reduced when attention was divided, even though behavioral performance suffered greatly. We then analyzed two word-selective regions along the occipito-temporal sulcus (OTS) of both hemispheres (i.e., sub-regions of visual word form area, VWFA). Unlike retinotopic cortex, each word-selective region responded to words on both sides of fixation. Nonetheless, a single region in the left hemisphere (VWFA-1 in posterior OTS) contained spatial channels for both hemifields that were independently modulated by selective attention. Thus, the left posterior VWFA supports parallel processing of multiple words. In contrast, a more anterior word-selective region in the left hemisphere (VWFA-2 in mid-OTS) showed limited spatial and attentional selectivity, consistent with activity of a single channel. Therefore, the visual system can process two words in parallel up to a late stage in the ventral stream. The transition from two parallel channels to a single channel in more anterior regions is consistent with the observed bottleneck in behavior.

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↗

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↗