Procenko O, Read JCA, Nityananda V ( 2024 )
Physically stressed bees expect less reward in an active choice judgement bias test

Vol: 291 (2032) Pages: https://doi.org/10.1098/rspb.2024.0512 [view on journal website] Pubmed ID : 39378898

Data is available here: https://rs.figshare.com/collections/Supplementary_material_from_Physically_Stressed_Bees_Expect_Less_Reward_in_an_Active_Choice_Judgement_Bias_Test_/7437275.

BBC news article.
Comment: Emotion-like states in animals are commonly assessed using judgment bias tests that measure judgements of ambiguous cues. Some studies have used these tests to argue for emotion-like states in insects. However, most of these results could have other explanations, including changes in motivation and attention. To control for these explanations, we developed a novel judgment bias test, requiring bumblebees to make an active choice indicating their interpretation of ambiguous stimuli. Bumblebees were trained to associate high or low rewards, in two different reward chambers, with distinct colours. We subsequently presented bees with ambiguous colours between the two learnt colours. In response, physically stressed bees were less likely than control bees to enter the reward chamber associated with high reward. Signal detection and drift diffusion models showed that stressed bees were more likely to choose low reward locations in response to ambiguous cues. The signal detection model further showed that the behaviour of stressed bees was explained by a reduction in the estimated probability of high rewards. We thus provide strong evidence for judgement biases in bees and suggest that their stress-induced behaviour is explained by reduced expectation of higher rewards, as expected for a pessimistic judgement bias.

Fernandez-Alonso M, Finch AP, Love GD, Read JCA ( 2024 )
Ocular accommodation and wavelength: The effect of longitudinal chromatic aberration on the stimulus–response curve

Journal of Vision Vol: 24; 11 Pages: [view on journal website] Pubmed ID : 38411958

Data for this article is available at https://doi.org/10.25405/data.ncl.23531250.v1. The zip file contains experimental data in the form of Matlab .mat files and .csv files. Code to process, analyse and plot these results are provided in a linked repository here: https://doi.org/10.25405/data.ncl.23522934.
Comment: The longitudinal chromatic aberration (LCA) of the eye creates a chromatic blur on the retina that is an important cue for accommodation. Although this mechanism can work optimally in broadband illuminants such as daylight, it is not clear how the system responds to the narrowband illuminants used by many modern displays. Here, we measured pupil and accommodative responses as well as visual acuity under narrowband light-emitting diode (LED) illuminants of different peak wavelengths. Observers were able to accommodate under narrowband light and compensate for the LCA of the eye, with no difference in the variability of the steady-state accommodation response between narrowband and broadband illuminants. Intriguingly, our subjects compensated more fully for LCA at nearer distances. That is, the difference in accommodation to different wavelengths became larger when the object was placed nearer the observer, causing the slope of the accommodation response curve to become shallower for shorter wavelengths and steeper for longer ones. Within the accommodative range of observers, accommodative errors were small and visual acuity normal. When comparing between illuminants, when accommodation was accurate, visual acuity was worst for blue narrowband light. This cannot be due to the sparser spacing for S-cones, as our stimuli had equal luminance and thus activated LM-cones roughly equally. It is likely because ocular LCA changes more rapidly at shorter wavelength and so the finite spectral bandwidth of LEDs corresponds to a greater dioptric range at shorter wavelengths. This effect disappears for larger accommodative errors, due to the increased depth of focus of the eye.

Read JCA, Maus G, Schor CM ( 2024 )
Understanding accommodative control in the clinic: Modeling latency and amplitude for uncorrected refractive error, presbyopia and cycloplegia

Journal of Vision Vol: 24 Pages: [view on journal website] Pubmed ID : 38488409

Code for this paper is available here/a> (https://doi.org/10.25405/data.ncl.21909279.v1)
Comment: Accommodation is the process of adjusting the eye's optical power so as to focus at different distances. Uncorrected refractive error and/or functional presbyopia mean that sharp focus may not be achievable for some distances, so observers experience sustained defocus. Here, we identify a problem with current models of accommodative control: They predict excessive internal responses to stimuli outside accommodative range, leading to unrealistic adaptation effects. Specifically, after prolonged exposure to stimuli outside range, current models predict long latencies in the accommodative response to stimuli within range, as well as unrealistic dynamics and amplitudes of accommodative vergence innervation driven by the accommodative neural controller. These behaviors are not observed empirically. To solve this issue, we propose that the input to blur-driven accommodation is not retinal defocus, but correctable defocus. Predictive models of accommodative control already estimate demand from sensed defocus, using a realistic “virtual plant” to estimate accommodation. Correctable defocus can be obtained by restricting this demand to values physically attainable by the eye. If we further postulate that correctable defocus is computed using an idealized virtual plant that retains a young accommodative range, we can explain why accommodative–convergence responses are observed for stimuli that are too near—but not too far—to focus on. We model cycloplegia as a change in gain, and postulate a form of neural myopia to explain the additional relaxation of accommodation often seen with cycloplegia. This model produces plausible predictions for the accommodative response and accommodative convergence signal in a wide range of clinically relevant situations

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Smulders TV, Read JCA ( 2024 )
Different memory systems in food-hoarding birds: A response to Pravosudov

Learning & Behavior Vol: Pages: [view on journal website] Pubmed ID : 38755512

Comment: We recently showed that food-hoarding birds use familiarity processes more than recollection processes when remembering the spatial location of their caches (Smulders et al., Animal Cognition 26:1929-1943, 2023). Pravosudov (Learning & Behavior, https://doi.org/ https://doi.org/10.3758/s13420-023-00616-x , 2023) called our findings into question, claiming that our method is unable to distinguish between recollection and familiarity, and that associative learning tasks are a better way to study the memory for cache sites. In this response, we argue that our methods would have been more likely to detect recollection than familiarity, if Pravosudov's assertions were correct. We also point out that associative learning mechanisms may be good for building semantic knowledge, but are incompatible with the needs of cache site memory, which requires the unique encoding of caching events.

Finch A, Fernandez-Alonso M, Kirby A, Read JCA, Love G ( 2024 )
Focusing on mixed narrow band stimuli: Implications for mechanisms of accommodation and displays

Journal of Vision Vol: 24 Pages: https://doi.org/10.1167/jov.24.9.14 [view on journal website] Pubmed ID : 39302649

Comment: The eye has considerable chromatic aberration, meaning that the accommodative demand varies with wavelength. Given this, how does the eye accommodate to light of differing spectral content? Previous work is not conclusive but, in general, the eye focuses in the center of the visible spectrum for broadband light, and it focuses at a distance appropriate for individual wavelengths for narrowband light. For stimuli containing two colors, there are also mixed reports. This is the second of a series of two papers where we investigate accommodation in relation to chromatic aberration Fernandez-Alonso, Finch, Love, and Read (2024). In this paper, for the first time, we measure how the eye accommodates to images containing two narrowband wavelengths, with varying relative luminance under monocular conditions. We find that the eye tends to accommodate between the two extremes, weighted by the relative luminance. At first sight, this seems reasonable, but we show that image quality would be maximized if the eye instead accommodated on the more luminous wavelength. Next we explore several hypotheses as to what signal the eye might be using to drive accommodation and compare these with the experimental data. We show that the data is best explained if the eye seeks to maximize contrast at low spatial frequencies. We consider the implication of these results for both the mechanism behind accommodation, and for modern displays containing narrowband illuminants.

Linton P, Morgan MJ, Read JCA, Vishwanath D, Creem-Regehr SH, Domini F ( 2023 )
New Approaches to 3D Vision

Philosophical Transactions of the Royal Society B: Biological Sciences Vol: 378(1869) Pages: 20210443 [view on journal website] Pubmed ID : 36511413

Comment: New approaches to 3D vision are enabling new advances in artificial intelligence and autonomous vehicles, a better understanding of how animals navigate the 3D world, and new insights into human perception in virtual and augmented reality. Whilst traditional approaches to 3D vision in computer vision (SLAM: simultaneous localization and mapping), animal navigation (cognitive maps), and human vision (optimal cue integration) start from the assumption that the aim of 3D vision is to provide an accurate 3D model of the world, the new approaches to 3D vision explored in this issue challenge this assumption. Instead, they investigate the possibility that computer vision, animal navigation, and human vision can rely on partial or distorted models or no model at all. This issue also highlights the implications for artificial intelligence, autonomous vehicles, human perception in virtual and augmented reality, and the treatment of visual disorders, all of which are explored by individual articles.

This article is part of a discussion meeting issue ‘New approaches to 3D vision’.

Read JCA ( 2023 )
Stereopsis without correspondence

Philosophical Transactions of the Royal Society B: Biological Sciences Vol: 378 Pages: 20210449 [view on journal website] Pubmed ID : 36511401

Matlab code is available at https://doi.org/10.25405/data.ncl.19487414.v1>https://doi.org/10.25405/data.ncl.19487414.v1.
Comment: Stereopsis has traditionally been considered a complex visual ability, restricted
to large-brained animals. The discovery in the 1980s that insects, too, have
stereopsis, therefore, challenged theories of stereopsis. How can such simple
brains see in three dimensions? A likely answer is that insect stereopsis has
evolved to produce simple behaviour, such as orienting towards the closer
of two objects or triggering a strike when prey comes within range. Scientific
thinking about stereopsis has been unduly anthropomorphic, for example
assuming that stereopsis must require binocular fusion or a solution of the
stereo correspondence problem. In fact, useful behaviour can be produced
with very basic stereoscopic algorithms which make no attempt to achieve
fusion or correspondence, or to produce even a coarse map of depth across
the visual field. This may explain why some aspects of insect stereopsis
seem poorly designed from an engineering point of view: for example,
paying no attention to whether interocular contrast or velocities match. Such
algorithms demonstrably work well enough in practice for their species, and
may prove useful in particular autonomous applications.
This article is part of a discussion meeting issue ‘New approaches to 3D
vision’.

Fernandez-Alonso M, Innes W, Read JCA ( 2023 )
Peripheral Flicker Fusion at High Luminance: Beyond the Ferry–Porter Law

Vision Vol: 7(1), 26 Pages: 1-16 [view on journal website]

. The data presented in the paper and the processed results are available in the Newcastle University research repository at https://doi.org/10.25405/data.ncl.21725336. The code used for the analyses and to generate the figures are also available here: https://doi.org/10.25405/data.ncl.21764885.
Comment: The relationship between luminous intensity and the maximum frequency of flicker that can be detected defines the limits of the temporal-resolving ability of the human visual system, and characterizing it has important theoretical and practical applications; particularly for determining the optimal refresh rate for visual displays that would avoid the visibility of flicker and other temporal artifacts. Previous research has shown that this relationship is best described by the Ferry–Porter law, which states that critical flicker fusion (CFF) increases as a linear function of log retinal illuminance. The existing experimental data showed that this law holds for a wide range of stimuli and up to 10,000 Trolands; however, beyond this, it was not clear if the CFF continued to increase linearly or if the function saturated. Our aim was to extend the experimental data available to higher light intensities than previously reported in the literature. For this, we measured the peripheral CFF at a range of illuminances over six orders of magnitude. Our results showed that for up to 104 Trolands, the data conformed to the Ferry–Porter law with a similar slope, as previously established for this eccentricity; however, at higher intensities, the CFF function flattens and saturates at ~90 Hz for a target size of 5.7 degrees, and at ~100 Hz for a target of 10 degrees of angular size. These experimental results could prove valuable for the design of brighter visual displays and illumination sources that are temporally modulated.

Vali M, Nazari B, Sadri S, Khalili Pour E, Riazi-Esfahani H, Faghihi H, Ebrahimiadib N, Azizkhani M, Innes W, Steel DH, Hurlbert AC, Read JCA, Kafieh R ( 2023 )
CNV-Net: Segmentation, Classification and Activity Score Measurement of Choroidal Neovascularization (CNV) Using Optical Coherence Tomography Angiography (OCTA)

Diagnostics Vol: 13(7) Pages: 10.3390/diagnostics13071309 [view on journal website]

Comment: This paper aims to present an artificial intelligence-based algorithm for the automated segmentation of Choroidal Neovascularization (CNV) areas and to identify the presence or absence of CNV activity criteria (branching, peripheral arcade, dark halo, shape, loop and anastomoses) in OCTA images. Methods: This retrospective and cross-sectional study includes 130 OCTA images from 101 patients with treatment-naïve CNV. At baseline, OCTA volumes of 6 × 6 mm2 were obtained to develop an AI-based algorithm to evaluate the CNV activity based on five activity criteria, including tiny branching vessels, anastomoses and loops, peripheral arcades, and perilesional hypointense halos. The proposed algorithm comprises two steps. The first block includes the pre-processing and segmentation of CNVs in OCTA images using a modified U-Net network. The second block consists of five binary classification networks, each implemented with various models from scratch, and using transfer learning from pre-trained networks. Results: The proposed segmentation network yielded an averaged Dice coefficient of 0.86. The individual classifiers corresponding to the five activity criteria (branch, peripheral arcade, dark halo, shape, loop, and anastomoses) showed accuracies of 0.84, 0.81, 0.86, 0.85, and 0.82, respectively. The AI-based algorithm potentially allows the reliable detection and segmentation of CNV from OCTA alone, without the need for imaging with contrast agents. The evaluation of the activity criteria in CNV lesions obtains acceptable results, and this algorithm could enable the objective, repeatable assessment of CNV features.

(This article belongs to the Special Issue Advances in Optical Coherence Tomography Angiography)

Plonkowski AT, Breakey RW, Read JCA, Sainsbury DCG ( 2023 )
The Use of Eye-tracking Technology in Cleft Lip: A Literature Review

Plastic and Reconstructive Surgery Global Open Vol: 11 Pages: e4980 [view on journal website] Pubmed ID : 37360237

Comment: Background: Eye-tracking has become an increasingly popular research tool within the field of cleft lip and/or palate (CL+/−P). Despite this, there are no standardized protocols for conducting research. Our objective was to conduct a literature review of the methodology and outcomes of previous publications using eye-tracking
in CL+/−P.
Methods: The PubMed, Google Scholar, and Cochrane databases were searched to identify all articles published up to August 2022. All articles were screened by two independent reviewers. Inclusion criteria included using eye-tracking, image stimuli of CL+/−P, and outcome reporting using areas of interest (AOIs). Exclusion criteria included non-English studies, conference articles, and image stimuli of conditions other than CL+/−P.
Results: Forty articles were identified, and 16 met the inclusion/exclusion criteria. Thirteen studies only displayed images of individuals following cleft lip surgery with three only displaying unrepaired cleft lips. Significant variation was found in study design, particularly in the AOIs used to report gaze outcomes. Ten studies asked participants to provide an outcome score alongside eye-tracking; however, only four compared outcome data to eye-tracking data. This review is primarily limited by the minimal number of publications in this area.
Conclusions: Eye-tracking can be a powerful tool in evaluating appearance outcomes following CL+/−P surgery. It is currently limited by the lack of standardized research methodology and varied study design. Before future work, a replicable protocol should be developed to maximize the potential of this technology.

Smulders TV, Douglas LJ, Reza D, Male LH, Prysce A, Alix A, de GuzmanDodd A, Read JCA ( 2023 )
Hoarding titmice predominantly use Familiarity, and not Recollection, when remembering cache locations

Animal Cognition Vol: 26 Pages: 1929–1943 [view on journal website] Pubmed ID : 37865619

The data presented in this paper, as well as all the individual ROC curves, can be found here: https://doi. org/10.25405/data.ncl.14938098.v1. The analysis code, including the code for ROC ftting can be found here: https://doi.org/10.25405/data. ncl.22710376.v1
Comment: Scatter-hoarding birds find their caches using spatial memory and have an enlarged hippocampus. Finding a cache site could be achieved using either Recollection (a discrete recalling of previously experienced information) or Familiarity (a feeling of "having encountered something before"). In humans, these two processes can be distinguished using receiver operating characteristic (ROC) curves. ROC curves for olfactory memory in rats have shown the hippocampus is involved in Recollection, but not Familiarity. We test the hypothesis that food-hoarding birds, having a larger hippocampus, primarily use Recollection to find their caches. We validate a novel method of constructing ROC curves in humans and apply this method to cache retrieval by coal tits (Periparus ater). Both humans and birds mainly use Familiarity in finding their caches, with lower contribution of Recollection. This contribution is not significantly different from chance in birds, but a small contribution cannot be ruled out. Memory performance decreases with increasing retention interval in birds. The ecology of food-hoarding Parids makes it plausible that they mainly use Familiarity in the memory for caches. The larger hippocampus could be related to associating cache contents and temporal context with cache locations, rather than Recollection of the spatial information itself.

Read JCA, Kaspiris-Rousellis C, Wood TS, Wu B, Vlaskamp BNS, Schor CM ( 2022 )
Seeing the future: Predictive control in neural models of ocular accommodation

Journal of Vision Vol: 22:9 Pages: https://doi.org/10.1167/jov.22.9.4 [view on journal website] Pubmed ID : 35925580

Code is available at https://doi.org/10.25405/data.ncl.14945550
Comment: Ocular accommodation is the process of adjusting the eye's crystalline lens so as to bring the retinal image into sharp focus. The major stimulus to accommodation is therefore retinal defocus, and in essence, the job of accommodative control is to send a signal to the ciliary muscle which will minimize the magnitude of defocus. In this article, we first provide a tutorial introduction to control theory to aid vision scientists without this background. We then present a unified model of accommodative control that explains properties of the accommodative response for a wide range of accommodative stimuli. Following previous work, we conclude that most aspects of accommodation are well explained by dual integral control, with a “fast” or “phasic” integrator enabling response to rapid changes in demand, which hands over control to a “slow” or “tonic” integrator which maintains the response to steady demand. Control is complicated by the sensorimotor latencies within the system, which delay both information about defocus and the accommodation changes made in response, and by the sluggish response of the motor plant. These can be overcome by incorporating a Smith predictor, whereby the system predicts the delayed sensory consequences of its own motor actions. For the first time, we show that critically-damped dual integral control with a Smith predictor accounts for adaptation effects as well as for the gain and phase for sinusoidal oscillations in demand. In addition, we propose a novel proportional-control signal to account for the power spectrum of accommodative microfluctuations during steady fixation, which may be important in hunting for optimal focus, and for the nonlinear resonance observed for low-amplitude, high-frequency input.

Nichol BAB, Hurlbert AC, Read JCA ( 2022 )
Predicting attitudes towards screening for neurodegenerative diseases using OCT and artificial intelligence: Findings from a literature review

Journal of Public Health Research Vol: 11(4) Pages: 1-12 [view on journal website]

Danesh H, Steel DH, Hogg J, Ashtari F, Innes WF, Bacardit, J, Hurlbert A, Read JCA, Kafieh R ( 2022 )
Synthetic OCT Data Generation to Enhance the Performance of Diagnostic Models for Neurodegenerative Diseases

Translational Vision Science and Technology Vol: 11(10) Pages: doi:https://doi.org/10.1167/tvst.11.10.10 [view on journal website]

Comment: Purpose: Optical coherence tomography (OCT) has recently emerged as a source for powerful biomarkers in neurodegenerative diseases such as multiple sclerosis (MS) and neuromyelitis optica (NMO). The application of machine learning techniques to the analysis of OCT data has enabled automatic extraction of information with potential to aid the timely diagnosis of neurodegenerative diseases. These algorithms require large amounts of labeled data, but few such OCT data sets are available now.

Methods: To address this challenge, here we propose a synthetic data generation method yielding a tailored augmentation of three-dimensional (3D) OCT data and preserving differences between control and disease data. A 3D active shape model is used to produce synthetic retinal layer boundaries, simulating data from healthy controls (HCs) as well as from patients with MS or NMO.

Results: To evaluate the generated data, retinal thickness maps are extracted and evaluated under a broad range of quality metrics. The results show that the proposed model can generate realistic-appearing synthetic maps. Quantitatively, the image histograms of the synthetic thickness maps agree with the real thickness maps, and the cross-correlations between synthetic and real maps are also high. Finally, we use the generated data as an augmentation technique to train stronger diagnostic models than those using only the real data.

Conclusions: This approach provides valuable data augmentation, which can help overcome key bottlenecks of limited data.

Translational Relevance: By addressing the challenge posed by limited data, the proposed method helps apply machine learning methods to diagnose neurodegenerative diseases from retinal imaging.

O’Keeffe J, Yap SH, Llamas-Cornejo I, Nityananda V, Read JCA ( 2022 )
A computational model of stereoscopic prey capture in praying mantises

PLOS Computational Biology Vol: 18(5) Pages: 1-33 [view on journal website] Pubmed ID : 35587948

ERRATA
Code for generating figures etc is here: https://doi.org/10.25405/data.ncl.17049413.v1
Comment: We present a simple model which can account for the stereoscopic sensitivity of praying mantis predatory strikes. The model consists of a single “disparity sensor”: a binocular neuron sensitive to stereoscopic disparity and thus to distance from the animal. The model is based closely on the known behavioural and neurophysiological properties of mantis stereopsis. The monocular inputs to the neuron reflect temporal change and are insensitive to contrast sign, making the sensor insensitive to interocular correlation. The monocular receptive fields have a excitatory centre and inhibitory surround, making them tuned to size. The disparity sensor combines inputs from the two eyes linearly, applies a threshold and then an exponent output nonlinearity. The activity of the sensor represents the model mantis’s instantaneous probability of striking. We integrate this over the stimulus duration to obtain the expected number of strikes in response to moving targets with different stereoscopic disparity, size and vertical disparity. We optimised the parameters of the model so as to bring its predictions into agreement with our empirical data on mean strike rate as a function of stimulus size and disparity. The model proves capable of reproducing the relatively broad tuning to size and narrow tuning to stereoscopic disparity seen in mantis striking behaviour. Although the model has only a single centre-surround receptive field in each eye, it displays qualitatively the same interaction between size and disparity as we observed in real mantids: the preferred size increases as simulated prey distance increases beyond the preferred distance. We show that this occurs because of a stereoscopic “false match” between the leading edge of the stimulus in one eye and its trailing edge in the other; further work will be required to find whether such false matches occur in real mantises. Importantly, the model also displays realistic responses to stimuli with vertical disparity and to pairs of identical stimuli offering a “ghost match”, despite not being fitted to these data. This is the first image-computable model of insect stereopsis, and reproduces key features of both neurophysiology and striking behaviour.

Read JCA ( 2021 )
Binocular Vision and Stereopsis Across the Animal Kingdom

Annual Review of Vision Science Vol: 7 Pages: 389-415 [view on journal website] Pubmed ID : 34283925

You can download this file direct from the Annual Reviews website using this link.
Comment: Most animals have at least some binocular overlap, i.e., a region of space that is viewed by both eyes. This reduces the overall visual field and raises the problem of combining two views of the world, seen from different vantage points, into a coherent whole. However, binocular vision also offers many potential advantages, including increased ability to see around obstacles and increased contrast sensitivity. One particularly interesting use for binocular vision is comparing information from both eyes to derive information about depth. There are many different ways in which this might be done, but in this review, I refer to them all under the general heading of stereopsis. This review examines the different possible uses of binocular vision and stereopsis and compares what is currently known about the neural basis of stereopsis in different taxa. Studying different animals helps us break free of preconceptions stemming from the way that stereopsis operates in human vision and provides new insights into the different possible forms of stereopsis.

Arranz-Paraiso S, Read JCA, Serrano-Pedraza I ( 2021 )
Reduced surround suppression in monocular motion perception

Journal of Vision Vol: 21, 10 Pages: https://doi.org/10.1167/jov.21.1.10 [view on journal website] Pubmed ID : 33450007

Comment: Motion discrimination of large stimuli is impaired at high contrast and short durations. This psychophysical result has been linked with the center-surround suppression found in neurons of area MT. Recent physiology results have shown that most frontoparallel MT cells respond more strongly to binocular than to monocular stimulation. Here we measured the surround suppression strength under binocular and monocular viewing. Thirty-nine participants took part in two experiments: (a) where the nonstimulated eye viewed a blank field of the same luminance (n = 8) and (b) where it was occluded with a patch (n = 31). In both experiments, we measured duration thresholds for small (1 deg diameter) and large (7 deg) drifting gratings of 1 cpd with 85% contrast. For each subject, a Motion Suppression Index (MSI) was computed by subtracting the duration thresholds in logarithmic units of the large minus the small stimulus. Results were similar in both experiments. Combining the MSI of both experiments, we found that the strength of suppression for binocular condition (MSIbinocular = 0.249 ± 0.126 log10 (ms)) is 1.79 times higher than under monocular viewing (MSImonocular = 0.139 ± 0.137 log10 (ms)). This increase is too high to be explained by the higher perceived contrast of binocular stimuli and offers a new way of testing whether MT neurons account for surround suppression. Potentially, differences in surround suppression reported in clinical populations may reflect altered binocular processing.

Rosner R, Tarawneh G, Lukyanova V, Read JCA ( 2020 )
Binocular responsiveness of projection neurons of the praying mantis optic lobe in the frontal visual field

Journal of Comparative Physiology A Vol: https://doi.org/10.1007/s00359-020-01405-x Pages: [view on journal website] Pubmed ID : 32088748

Comment: Praying mantids are the only insects proven to have stereoscopic vision (stereopsis): the ability to perceive depth from the slightly shifted images seen by the two eyes. Recently, the first neurons likely to be involved in mantis stereopsis were described and a speculative neuronal circuit suggested. Here we further investigate classes of neurons in the lobula complex of the praying mantis brain and their tuning to stereoscopically-defined depth. We used sharp electrode recordings with tracer injections to identify visual projection neurons with input in the optic lobe and output in the central brain. In order to measure binocular response fields of the cells the animals watched a vertical bar stimulus in a 3D insect cinema during recordings. We describe the binocular tuning of 19 neurons projecting from the lobula complex and the medulla to central brain areas. The majority of neurons (12/19) were binocular and had receptive fields for both eyes that overlapped in the frontal region. Thus, these neurons could be involved in mantis stereopsis. We also find that neurons preferring different contrast polarity (bright vs dark) tend to be segregated in the mantis lobula complex, reminiscent of the segregation for small targets and widefield motion in mantids and other insects.

Serrano-Pedraza I, Vancleef K, Herbert W, Goodship N, Woodhouse M, Read JCA ( 2020 )
Efficient estimation of stereo thresholds: What slope should be assumed for the psychometric function?

PLOS ONE Vol: Pages: [view on journal website] Pubmed ID : 31895925

Comment: Bayesian staircases are widely used in psychophysics to estimate detection thresholds. Simulations have revealed the importance of the parameters selected for the assumed subject's psychometric function in enabling thresholds to be estimated with small bias and high precision. One important parameter is the slope of the psychometric function, or equivalently its spread. This is often held fixed, rather than estimated for individual subjects, because much larger numbers of trials are required to estimate the spread as well as the threshold. However, if this fixed value is wrong, the threshold estimate can be biased. Here we determine the optimal slope to minimize bias and maximize precision when measuring stereoacuity with Bayesian staircases. We performed 2- and 4AFC disparity detection stereo experiments in order to measure the spread of the disparity psychometric function in human observers assuming a Logistic function. We found a wide range, between 0.03 and 3.5 log10 arcsec, with little change with age. We then ran simulations to examine the optimal spread using the empirical data. From our simulations and for three different experiments, we recommend selecting assumed spread values between the percentiles 60-80% of the population distribution of spreads (these percentiles can be extended to other type of thresholds). For stereo thresholds, we recommend a spread around the value σ = 1.7 log10 arcsec for 2AFC (slope β = 4.3 /log10 arcsec), and around σ = 1.5 log10 arcsec for 4AFC (β = 4.9 /log10 arcsec). Finally, we compared a Bayesian procedure (ZEST using the optimal σ) with five Bayesian procedures that are versions of ZEST-2D, Psi, and Psi-marginal. In general, for the conditions tested, ZEST optimal σ showed the lowest threshold bias and highest precision.

Casanova T, Black C, Rafiq S, Hugill-Jones J, Read JCA, Vancleef K ( 2020 )
The impact of active research involvement of young children in the design of a new stereotest

Research Involvement and Engagement Vol: 6 (29) Pages: https://doi.org/10.1186/s40900-020-00194-6 [view on journal website]

Comment: Background: Although considered important, the direct involvement of young children in research design is scarce and to our knowledge its impact has never been measured. We aim to demonstrate impact of young children’s involvement in improving the understanding of a new 3D eye test or stereotest.
Methods: After a pre-measure of understanding was taken, we explored issues with the test instructions in patient and public involvement (PPI) sessions where children acted as advisers in the test design. Feedback was collected via observations, rating scales and verbal comments. An interdisciplinary panel reviewed the feedback, discussed potential changes to the test design, and decided on the implementation. Subsequently, a post-measure of understanding (Study 1–2) and engagement (Study 3) was collected in a pre-post study design. Six hundred fifty children (2–11.8 years old) took part in the pre-measure, 111 children (1–12 years old) in the subsequent PPI sessions, and 52 children (4–6 years old) in the first post-measure. One hundred twenty-two children (1–12 years old) and unrelated adults took then part in a second series of PPI sessions, and 53 people (2–39 years old) in the final post-measure. Adults were involved to obtain verbal descriptions of the target that could be used to explain the task to children.
Results: Following feedback in Study 1, we added a frame cue and included a shuffle animation. This increased the percentage of correct practice trials from 76 to 97% (t (231) = 14.29, p < .001), but more encouragements like ‘Keep going!’ were needed (t (64) = 8.25, p < .001). After adding a cardboard demo in Study 2, the percentage of correct trials remained stable but the number of additional instructions given decreased (t (103) = 3.72, p < .001) as did the number of encouragements (t (103) = 8.32, p < .001). Therefore, changes in test design following children’s feedback significantly improved task understanding.
Conclusions: Our study demonstrates measurable impact of involvement of very young children in research design through accessible activities. The changes implemented following their feedback significantly improved the understanding of our test. Our approach can inform researchers on how to involve young children in research design and can contribute to developing guidelines for involvement of young children in research.

McCaslin AG, Vancleef K, Hubert L, Read JCA, Port NL ( 2020 )
Stereotest Comparison: Efficacy, Reliability, and Variability of a New Glasses-Free Stereotest

Translational Vision Science and Technology Vol: 9 (9) Pages: https://doi.org/10.1167/tvst.9.9.29 [view on journal website] Pubmed ID : 32879785

Comment: Purpose: To test the validity of the ASTEROID stereotest as a clinical test of depth perception by comparing it to clinical and research standard tests.
Methods: Thirty-nine subjects completed four stereotests twice: the ASTEROID test on an autostereo 3D tablet, a research standard on a VPixx PROPixx 3D projector, Randot Circles, and Randot Preschool. Within 14 days, subjects completed each test for a third time.
Results: ASTEROID stereo thresholds correlated well with research standard thresholds (r = 0.87, P < 0.001), although ASTEROID underestimated standard threshold (mean difference = 11 arcsec). ASTEROID results correlated less strongly with Randot Circles (r = 0.54, P < 0.001) and Randot Preschool (r = 0.64, P < 0.001), due to the greater measurement range of ASTEROID (1–1000 arcsec) compared to Randot Circles or Randot Preschool. Stereo threshold variability was low for all three clinical stereotests (Bland–Altman 95% limits of agreement between test and retest: ASTEROID, ±0.37; Randot Circles, ±0.24; Randot Preschool, ±0.23). ASTEROID captured the largest range of stereo in a normal population with test–retest reliability comparable to research standards (immediate r = 0.86 for ASTEROID vs. 0.90 for PROPixx; follow-up r = 0.68 for ASTEROID vs. 0.88 for PROPixx).
Conclusions: Compared to clinical and research standards for assessing depth perception, ASTEROID is highly accurate, has good test–retest reliability, and measures a wider range of stereo threshold.

Translational Relevance: The ASTEROID stereotest is a better clinical tool for determining baseline stereopsis and tracking changes during treatment for amblyopia and strabismus compared to current clinical tests.

Read JCA, Wong ZY, Yek X, Wong YX, Bachtoula O, Llamas-Cornejo I, Serrano-Pedraza ( 2020 )
ASTEROID stereotest v1.0: lower stereo thresholds using smaller, denser and faster dots

Ophthalmic and Physiological Optics Vol: https://doi.org/10.1111/opo.12737 Pages: [view on journal website] Pubmed ID : 32989799

Analysis code and data files are available at https://doi.org/10.25405/data.ncl.11815845.
Comment: Purpose: In 2019, we described ASTEROID, a new stereotest run on a 3D tablet
computer which involves a four-alternative disparity detection task on a dynamic
random-dot stereogram. Stereo thresholds measured with ASTEROID were well
correlated with, but systematically higher than (by a factor of around 1.5), thresholds
measured with previous laboratory stereotests or the Randot Preschool clinical
stereotest. We speculated that this might be due to the relatively large, sparse
dots used in ASTEROID v0.9. Here, we introduce and test the stereo thresholds
and test-repeatability of the new ASTEROID v1.0, which uses precomputed
images to allow stereograms made up of much smaller, denser dots.
Methods: Stereo thresholds and test/retest repeatability were tested and compared
between the old and new versions of ASTEROID (n = 75) and the Randot Circles
(n = 31) stereotest, in healthy young adults.
Results: Thresholds on ASTEROID v1.0 are lower (better) than on ASTEROID
v0.9 by a factor of 1.4, and do not differ significantly from thresholds on the Randot
Circles. Thresholds were roughly log-normally distributed with a mean of
1.54 log10 arcsec (35 arcsec) on ASTEROID v1.0 compared to 1.70 log10 arcsec
(50 arcsec) on ASTEROID v0.9. The standard deviation between observers was
the same for both versions, 0.32 log10 arcsec, corresponding to a factor of 2 above
and below the mean. There was no difference between the versions in their test/
retest repeatability, with 95% coefficient of repeatability = 0.46 log10 arcsec (a
factor of 2.9 or 1.5 octaves) and a Pearson correlation of 0.8 (comparable to other
clinical stereotests).
Conclusion: The poorer stereo thresholds previously reported with ASTEROID
v0.9 appear to have been due to the relatively large, coarse dots and low density
used, rather than to some other aspect of the technology. Employing the small
dots and high density used in ASTEROID v1.0, thresholds and test/retest repeatability
are similar to other clinical stereotests.

Fernandez-Alonso M, Kaspiris-Rousellis C, Innes W, Read JCA ( 2019 )
Assessment of Psychophysical Methods for Measuring the Critical Flicker Fusion Frequency in Yes/No Tasks

Proceedings of the European Light Field Imaging Conference (European Association for Signal Processing) Vol: Pages: [view on journal website]

Comment: The Critical Flicker Fusion (CFF) threshold is widely used to evaluate the limits of visual temporal processing and has important practical applications in the field of display technologies. In this study, we evaluate the suitability of a novel adaptive psychophysical procedure for measuring CFF thresholds in a YES/NO task. Our results indicate that while the adaptive staircase procedure has high repeatability and is of shorter
duration when compared to the more robust constant stimuli method, its accuracy is lower, giving thresholds that were significantly higher (p<0.01) by approximately 15Hz.

Kaspiris-Rousellis C, Fernandez-Alonso M, Read JCA ( 2019 )
Extending the Human Foveal Spatial Contrast Sensitivity Function to High Luminance Range

Proceedings of the European Light Field Imaging Conference (European Association for Signal Processing) Vol: Pages: [view on journal website]

Comment: The human contrast sensitivity function (CSF) is the most general way of quantifying what human vision can perceive. It predicts which artifacts will be visible on a display and what changes to hardware will result in noticeable improvements. Contrast sensitivity varies with luminance, and as new technology is producing higher luminance range displays, it is becoming essential to understand how the CSF behaves in this regime. Following this direction, we investigated the effect of adaptation luminance on contrast sensitivity for sine-wave gratings over a large number of CSF measurements in the literature. We examined the validity of the linear to DeVries-Rose to Weber region transition that is usually assumed to predict this relationship. We found a gradual transition among the three regions with steeper/flatter slopes for higher/lower frequencies and lower/higher retinal illuminance. A further decreasing region was located at low to intermediate frequencies, which was consistent across studies. Based on this theoretical construct, we adopted a CSF model consisting of central elements in the human visual signal processing and three limiting internal noise components corresponding to each region. We assessed the model’s performance on the measured contrast sensitivities and proposed an eight-parameter form to describe the contrast sensitivity surface in the spatial frequency-luminance domain.

Nityananda V, O’Keeffe J, Umeton D, Simmons A, Read JCA ( 2019 )
Second-order cues to figure motion enable object detection during prey capture by praying mantises

PNAS Vol: Pages: [view on journal website] Pubmed ID : 31818943

Full data and analysis code here on Figshare.
Comment: Detecting motion is essential for animals to perform a wide variety of functions. In order to do so, animals could exploit motion cues, including both first-order cues—such as luminance correlation over time—and second-order cues, by correlating higher-order visual statistics. Since first-order motion cues are typically sufficient for motion detection, it is unclear why sensitivity to second-order motion has evolved in animals, including insects. Here, we investigate the role of second-order motion in prey capture by praying mantises. We show that prey detection uses second-order motion cues to detect figure motion. We further present a model of prey detection based on second-order motion sensitivity, resulting from a layer of position detectors feeding into a second layer of elementary-motion detectors. Mantis stereopsis, in contrast, does not require figure motion and is explained by a simpler model that uses only the first layer in both eyes. Second-order motion cues thus enable prey motion to be detected, even when perfectly matching the average background luminance and independent of the elementary motion of any parts of the prey. Subsequent to prey detection, processes such as stereopsis could work to determine the distance to the prey. We thus demonstrate how second-order motion mechanisms enable ecologically relevant behavior such as detecting camouflaged targets for other visual functions including stereopsis and target tracking.

Read JCA, Rafiq S, Hugill J, Casanova T, Black C, O'Neill A, Puyat V, Haggerty H, Smart K, Powell C, Taylor K, Clarke MP, Vancleef K ( 2019 )
Characterizing the Randot Preschool stereotest: Testability, norms, reliability, specificity and sensitivity in children aged 2-11 years

PLOS ONE Vol: 14(11) Pages: [view on journal website] Pubmed ID : 31697704

Note - to fit within filesize limits, I've had to upload a version with compressed images. Since the original is freely available, I suggest you download it directly from the journal website.

Data and analysis code are available here.
Comment: Purpose
To comprehensively assess the Randot Preschool stereo test in young children, including testability, normative values, test/retest reliability and sensitivity and specificity for detecting binocular vision disorders.

Methods
We tested 1005 children aged 2–11 years with the Randot Preschool stereo test, plus a cover/uncover test to detect heterotropia. Monocular visual acuity was assessed in both eyes using Keeler Crowded LogMAR visual acuity test for children aged 4 and over.

Results
Testability was very high: 65% in two-year-olds, 92% in three-year-olds and ~100% in older children. Normative values: In 389 children aged 2–5 with apparently normal vision, 6% of children scored nil (stereoblind). In those who obtained a threshold, the mean log threshold was 2.06 log10 arcsec, corresponding to 114 arcsec, and the median threshold was 100 arcsec. Most older children score 40 arcsec, the best available score. We found a small sex difference, with girls scoring slightly but significantly better. Test/retest reliability: ~99% for obtaining any score vs nil. Agreement between stereo thresholds is poor in children aged 2–5; 95% limit of agreement = 0.7 log10 arcsec: five-fold change in stereo threshold may occur without any change in vision. In children over 5, the test essentially acts only as a binary classifier since almost all non-stereoblind children score 40 arcsec. Specificity (true negative rate): >95%. Sensitivity (true positive rate): poor, <50%, i.e. around half of children with a demonstrable binocular vision abnormality score well on the Randot Preschool.

Conclusions
The Randot Preschool is extremely accessible for even very young children, and is very reliable at classifying children into those who have any stereo vision vs those who are stereoblind. However, its ability to quantify stereo vision is limited by poor repeatability in children aged 5 and under, and a very limited range of scores relevant to children aged over 5.

Figures

Nityananda V, Joubier C, Tan J, Tarawneh G, Read JCA ( 2019 )
Motion-in-depth perception and prey capture in the praying mantis Sphodromantis lineola

Journal of Experimental Biology Vol: 222 Pages: jeb198614 [view on journal website] Pubmed ID : 31064852

Data and analysis code on figshare.
Comment: Perceiving motion-in-depth is essential to detecting approaching
or receding objects, predators and prey. This can be achieved
using several cues, including binocular stereoscopic cues such
as changing disparity and interocular velocity differences, and
monocular cues such as looming. Although these have been
studied in detail in humans, only looming responses have been well
characterized in insects and we know nothing about the role of
stereoscopic cues and how they might interact with looming cues. We
used our 3D insect cinema in a series of experiments to investigate
the role of the stereoscopic cues mentioned above, as well as
looming, in the perception of motion-in-depth during predatory strikes
by the praying mantis Sphodromantis lineola. Our results show that
motion-in-depth does increase the probability of mantis strikes but
only for the classic looming stimulus, an expanding luminance edge.
Approach indicated by radial motion of a texture or expansion of a
motion-defined edge, or by stereoscopic cues, all failed to elicit
increased striking. We conclude that mantises use stereopsis to
detect depth but not motion-in-depth, which is detected via looming.

Umeton D, Tarawneh G, Fezza E, Read JCA, Rowe C ( 2019 )
Pattern and Speed Interact to Hide Moving Prey

Current Biology Vol: 29(18) Pages: 3109-3113.e3 [view on journal website] Pubmed ID : 31522941

Comment article by Johannes Zanker: "Prey capture: Becoming invisible when you move"

Newcastle University press release: "It's all a blur: why stripes hide moving prey" Media coverage: ITV news; The Sun Article on The Conversation website.

Raw data and analysis code are available here: https://doi.org/10.25405/data.ncl.8869919.
Software to run the experiments is here: https://github.com/m3project.

Comment: Evolutionary biologists have long been fascinated by camouflage patterns that help animals reduce their chances of being detected by predators. However, patterns that hide prey when they remain stationary, such as those that match their backgrounds, are rendered ineffective once prey are moving. The question remains: can a moving animal ever be patterned in a way that helps reduce detection by predators? One long-standing idea is that high-contrast patterns with repeated elements, such as stripes, which are highly visible when prey are stationary, can actually conceal prey when they move fast enough [11, 12, 13, 14]. This is predicted by the “flicker fusion effect,” which occurs when prey move with sufficient speed that their pattern appears to blur, making them appear more featureless and become less conspicuous against the background [2, 8]. However, although this idea suggests a way to camouflage moving prey, it has not been empirically tested, and it is not clear that it would work at speeds that are biologically relevant to a predator [13]. Combining psychophysics and behavioral approaches, we show that speed and pattern interact to determine the detectability of prey to the praying mantis (Sphodromantis lineola) and, crucially, that prey with high-contrast stripes become less visible than prey with background-matching patterns when moving with sufficient speed. We show that stripes can reduce the detection of moving prey by exploiting the spatiotemporal limitations of predator perception, and that the camouflaging effect of a pattern depends upon the speed of prey movement.

Rosner R, von Hadeln J, Tarawneh G, Read JCA ( 2019 )
A neuronal correlate of insect stereopsis

Nature Communications Vol: 10(1):2845 Pages: 1-9 [view on journal website] Pubmed ID : 31253782

Short film by Nature Video about the project.

Newcastle University press release; Newcastle Chronicle; Edgy.app

Reconstructed neurons are available through NeuroMorpho.Org here: https://doi.org/10.13021/ay7p-fw49.
Neurophysiological data along with code to analyse data, implement the model neurons and generate figures are here: https://doi.org/10.25405/data.ncl.8063327.

Comment: A puzzle for neuroscience-and robotics-is how insects achieve surprisingly complex behaviours with such tiny brains. One example is depth perception via binocular stereopsis in the praying mantis, a predatory insect. Praying mantids use stereopsis, the computation of distances from disparities between the two retinal images, to trigger a raptorial strike of their forelegs when prey is within reach. The neuronal basis of this ability is entirely unknown. Here we show the first evidence that individual neurons in the praying mantis brain are tuned to specific disparities and eccentricities, and thus locations in 3D-space. Like disparity-tuned cortical cells in vertebrates, the responses of these mantis neurons are consistent with linear summation of binocular inputs followed by an output nonlinearity. Our study not only proves the existence of disparity sensitive neurons in an insect brain, it also reveals feedback connections hitherto undiscovered in any animal species.

Read JCA ( 2019 )
Visual Perception: Monovision Can Bias the Apparent Depth of Moving Objects

Current Biology Vol: 29(15) Pages: PR738-R740 [view on journal website]

Comment: ‘Monovision’ — using one eye for near work and one for distance — is a common alternative to reading
glasses. New work shows that monovision can cause the distance of moving objects to be misestimated,
with potentially serious consequences

Read JCA, Cumming BG ( 2019 )
The psychophysics of stereopsis can be explained without invoking independent ON and OFF channels

Journal of Vision Vol: 19(6):7 Pages: 1-14 [view on journal website] Pubmed ID : 31173632

Comment: Early vision proceeds through distinct ON and OFF channels, which encode luminance increments and decrements respectively. It has been argued that these channels also contribute separately to stereoscopic vision. This is based on the fact that observers perform better on a noisy disparity discrimination task when the stimulus is a random-dot pattern consisting of equal numbers of black and white dots (a “mixed-polarity stimulus”, argued to activate both ON and OFF stereo channels), than when it consists of all-white or all-black dots (“same-polarity”, argued to activate only one). However, it is not clear how this theory can be reconciled with our current understanding of disparity encoding. Recently, a binocular convolutional neural network was able to replicate the mixed-polarity advantage shown by human observers, even though it was based on linear filters and contained no mechanisms which would respond separately to black or white dots. Here, we show that a subtle feature of the way the stimuli were constructed in all these experiments can explain the results. The interocular correlation between left and right images is actually lower for the same-polarity stimuli than for mixed-polarity stimuli with the same amount of disparity noise applied to the dots. Since our current theories suggest stereopsis is based on a correlation-like computation in primary visual cortex, this can explain why performance was better for the mixed-polarity stimuli. We conclude that there is currently no evidence supporting separate ON and OFF channels in stereopsis.

Vancleef K, Serrano-Pedraza I, Sharp C, Slack G, Black C, Casanova T, Hugill J, Rafiq S, Burridge J, Puyat V, Ewane Enongue J, Gale H, Akotei H, Collier Z, Haggerty H, Smart K, Powell C, Taylor K, Clarke MP, Morgan G, Read JCA ( 2019 )
ASTEROID: A New Clinical Stereotest on an Autostereo 3D Tablet

Translational Vision Science and Technology Vol: 8(1): 25 Pages: 1-24 [view on journal website] Pubmed ID : 30834173

Comment: Purpose: To describe a new stereotest in the form of a game on an autostereoscopic
tablet computer designed to be suitable for use in the eye clinic and present data on
its reliability and the distribution of stereo thresholds in adults.
Methods: Test stimuli were four dynamic random-dot stereograms, one of which
contained a disparate target. Feedback was given after each trial presentation. A
Bayesian adaptive staircase adjusted target disparity. Threshold was estimated from the
mean of the posterior distribution after 20 responses. Viewing distance was monitored
via a forehead sticker viewed by the tablet’s front camera, and screen parallax was
adjusted dynamically so as to achieve the desired retinal disparity.
Results: The tablet must be viewed at a distance of greater than ~35 cm to produce a
good depth percept. Log thresholds were roughly normally distributed with a mean
of 1.75 log10 arcsec ¼ 56 arcsec and SD of 0.34 log10 arcsec ¼ a factor of 2.2. The
standard deviation agrees with previous studies, but ASTEROID thresholds are
approximately 1.5 times higher than a similar stereotest on stereoscopic 3D TV or on
Randot Preschool stereotests. Pearson correlation between successive tests in same
observer was 0.80. Bland-Altman 95% limits of reliability were 60.64 log10 arcsec ¼ a
factor of 4.3, corresponding to an SD of 0.32 log10 arcsec on individual threshold
estimates. This is similar to other stereotests and close to the statistical limit for 20
responses.
Conclusions: ASTEROID is reliable, easy, and portable and thus well-suited for clinical
stereoacuity measurements.
Translational Relevance: New 3D digital technology means that research-quality
psychophysical measurement of stereoacuity is now feasible in the clinic.

Vancleef K, Read JCA ( 2019 )
Which Stereotest do You Use? A Survey Research Study in the British Isles, the United States and Canada

British and Irish Orthoptic Journal Vol: 15(1) Pages: 15–24 [view on journal website]

Comment: A wide range of stereotests are available to measure stereopsis. Because each test has its own advantages and disadvantages, opinions differ on which is the preferred test to use in clinical practice. We conducted surveys comparing the use of stereotests in the British Isles and in the United States and Canada.
Two online surveys were developed following consultation with eye care professionals, one for each geographical area. Both surveys included two questions on the frequency of use of different stereotests, two questions on best practice stereotests, and two questions on the usefulness of stereotests. Researchers made distinctions between appointments with children below or above 6 years old for respondents from the British Isles and below or above 5 years old for respondents from the Unites Stated and Canada. The surveys were distributed through professional organisations.
We found Frisby to be the most used stereotest on the British Isles for both age groups. In the US and Canada, Titmus and Randot stereotest are more frequently used. Respondents consider these tests as the best practice stereotests. Eye care professionals agree stereotests are useful in the diagnosis and treatment decision making and even more so in obtaining an accurate measure of stereoacuity, especially with older children.

Tarawneh G, Nityananda V, Rosner R, Errington S, Herbert W, Arranz-Paraíso S, Busby N, Tampin J, Read JCA, Serrano-Pedraza I ( 2018 )
Contrast thresholds reveal different visual masking functions in humans and praying mantises

Biology Open Vol: 7(4). Pages: pii: bio029439. doi: 10.1242/bio.029439. [view on journal website] Pubmed ID : 29700198

Comment: Recently, we showed a novel property of the Hassenstein–Reichardt detector, namely that insect motion detection can be masked by ‘undetectable’ noise, i.e. visual noise presented at spatial frequencies at which coherently moving gratings do not elicit a response (Tarawneh et al., 2017). That study compared the responses of human and insect motion detectors using different ways of quantifying masking (contrast threshold in humans and masking tuning function in insects). In addition, some adjustments in experimental procedure, such as presenting the stimulus at a short viewing distance, were necessary to elicit a response in insects. These differences offer alternative explanations for the observed difference between human and insect responses to visual motion noise. Here, we report the results of new masking experiments in which we test whether differences in experimental paradigm and stimulus presentation between humans and insects can account for the undetectable noise effect reported earlier. We obtained contrast thresholds at two signal and two noise frequencies in both humans and praying mantises (Sphodromantis lineola), and compared contrast threshold differences when noise has the same versus different spatial frequency as the signal. Furthermore, we investigated whether differences in viewing geometry had any qualitative impact on the results. Consistent with our earlier finding, differences in contrast threshold show that visual noise masks much more effectively when presented at signal spatial frequency in humans (compared to a lower or higher spatial frequency), while in insects, noise is roughly equivalently effective when presented at either the signal spatial frequency or lower (compared to a higher spatial frequency). The characteristic difference between human and insect responses was unaffected by correcting for the stimulus distortion caused by short viewing distances in insects. These findings constitute stronger evidence that the undetectable noise effect reported earlier is a genuine difference between human and insect motion processing, and not an artefact caused by differences in experimental paradigms.

Vancleef K, Read JCA, Herbert W, Goodship N, Woodhouse M, Serrano-Pedraza I ( 2018 )
Two choices good, four choices better: For measuring stereoacuity in children, a four-alternative forced-choice paradigm is more efficient than two

PLoS ONE Vol: 13(7): e0201366 Pages: 1-15 [view on journal website] Pubmed ID : 30059524

Comment: Purpose
Measuring accurate thresholds in children can be challenging. A typical psychophysical
experiment is usually too long to keep children engaged. However, a reduction in the number of trials decreases the precision of the threshold estimate. We evaluated the efficiency
of forced-choice paradigms with 2 or 4 alternatives (2-AFC, 4-AFC) in a disparity detection
experiment. 4-AFC paradigms are statistically more efficient, but also more cognitively
demanding, which might offset their theoretical advantage in young children.
Methods
We ran simulations evaluating bias and precision of threshold estimates of 2-AFC and 4-
AFC paradigms. In addition, we measured disparity thresholds in 43 children (aged 6 to 17
years) with a 4-AFC paradigm and in 49 children (aged 4 to 17 years) with a 2-AFC paradigm, both using an adaptive weighted one-up one-down staircase.
Results
Simulations indicated a similar bias and precision for a 2-AFC paradigm with double the number of trials as a 4-AFC paradigm. On average, estimated threshold of the simulated data was equal to the model threshold, indicating no bias. The precision was improved with an increasing number of trials. Likewise, our data showed a similar bias and precision for a 2-AFC paradigm with 60 trials as for a 4-AFC paradigm with 30 trials. Trials in the 4-AFC paradigm took slightly longer as participants scanned more alternatives. However, the 4-AFC task still ended up faster for a given precision.
Conclusion
Bias and precision were similar in a 4-AFC task compared to a 2-AFC task with double the number of trials. However, a 4-AFC paradigm was more time efficient and is therefore recommended

Tarawneh G, Jones L, Nityananda V, Rosner R, Rind C, Read JCA ( 2018 )
Apparent Motion Perception in the Praying Mantis: Psychophysics and Modelling

Vision Vol: 2(3) Pages: 32; doi: 10.3390/vision2030032 [view on journal website]

The data collected in this study are available on https://github.com/m3project/mantis-dmax.
Comment: Apparent motion is the perception of motion created by rapidly presenting still frames in which objects are displaced in space. Observers can reliably discriminate the direction of apparent motion when inter-frame object displacement is below a certain limit, Dmax. Earlier studies of motion perception in humans found that Dmax is lower-bounded at around 15 arcmin, and thereafter scales with the size of the spatial elements in the images. Here, we run corresponding experiments in the praying mantis Sphodromantis lineola to investigate how Dmax scales with the element size. We use random moving chequerboard patterns of varying element and displacement step sizes to elicit the optomotor response, a postural stabilization mechanism that causes mantids to lean in the direction of large-field motion. Subsequently, we calculate Dmax as the displacement step size corresponding to a 50% probability of detecting an optomotor response in the same direction as the stimulus. Our main findings are that the mantis Dmax scales roughly as a square-root of element size and that, in contrast to humans, it is not lower-bounded. We present two models to explain these observations: a simple high-level model based on motion energy in the Fourier domain and a more-detailed one based on the Reichardt Detector. The models present complementary intuitive and physiologically-realistic accounts of how Dmax scales with the element size in insects. We conclude that insect motion perception is limited by only a single stage of spatial filtering, reflecting the optics of the compound eye. In contrast, human motion perception reflects a second stage of spatial filtering, at coarser scales than imposed by human optics, likely corresponding to the magnocellular pathway. After this spatial filtering, mantis and human motion perception and Dmax are qualitatively very similar.

Nityananda V, Tarawneh G, Henriksen S, Umeton D, Simmons A, Read JCA ( 2018 )
A Novel Form of Stereo Vision in the Praying Mantis

Current Biology Vol: 28 (4) Pages: 588-593.E4 [view on journal website] Pubmed ID : 29429616

Watch our video abstract here.

Data and analysis code on figshare

Media coverage: Ed Yong in The Atlantic, Digital Trends, Gizmodo, Sky News, Newsweek, Science Magazine, Popular Mechanics, The Telegraph, The Verge, Live Science, Science Alert, National Geographic.

Comment: Stereopsis is the ability to estimate distance based on the different views seen in the two eyes. It is an important model perceptual system in neuroscience and a major area of machine vision. Mammalian, avian, and almost all machine stereo algorithms look for similarities between the luminance-defined images in the two eyes, using a series of computations to produce a map showing how depth varies across the scene. Stereopsis has also evolved in at least one invertebrate, the praying mantis. Mantis stereopsis is presumed to be simpler than vertebrates’, but little is currently known about the underlying computations. Here, we show that mantis stereopsis uses a fundamentally different computational algorithm from vertebrate stereopsis --
rather than comparing luminance in the two eyes’ images directly, mantis stereopsis looks for regions of the images where luminance is changing. Thus, while there is no evidence that mantis stereopsis works at all with static images, it successfully reveals the distance to a moving target even in complex visual scenes with targets that are perfectly camouflaged against the background in terms of texture. Strikingly, these insects outperform human observers at judging stereoscopic distance when the pattern of luminance in the two eyes does not match. Insect stereopsis has thus evolved to be computationally efficient while being robust to poor image resolution and to discrepancies in the pattern of luminance between the two eyes.

Elliott A, Vancleef K ( 2018 )
Latest research on amblyopia treatment

Optician Vol: 26 January 2018 Pages: 26-27

Comment: Adele Elliott and Dr Kathleen Vancleef offer a review of current thinking in the management of amblyopia.

Vancleef K, Read JCA ( 2017 )
Measuring near stereopsis

Optician Vol: 10 November 2017 Pages: 26-27

Comment: Dr Kathleen Vancleef and Professor Jenny Read discuss stereopsis and how it is best assessed clinically. (C58138,
one distance learning CET point suitable for optometrists and dispensing opticians).

Umeton D, Read JCA, Rowe C ( 2017 )
Unravelling the illusion of flicker fusion

Biology Letters Vol: 13 Pages: 13: 20160831. [view on journal website] Pubmed ID : 28148834

Comment: For over 150 years, researchers have investigated the anti-predator function of animal patterns. However, this work has mainly focused on when prey remain still, and has only recently started to incorporate motion into the study of defensive coloration. As motion breaks camouflage, a new challenge is to understand how prey avoid predators while moving around their environment, and if a moving prey can ever be camouflaged. We propose that there is a solution to this, in that a ‘flicker fusion effect’ can change the appearance of the prey in the eyes of their predators to reduce the chances of initial detection. This effect occurs when a high contrast pattern blurs at speed, changing the appearance of the prey, which may help them better match their background. Despite being widely discussed in the literature, the flicker fusion effect is poorly described, there is no clear theoretical framework for testing how it might reduce predation, and the terminology describing it is, at best, rather confusing. Our review addresses these three key issues to enable researchers to formulate precise predictions about when the flicker fusion effect occurs, and to test how it can reduce predation.

Hands P ( 2017 )
Hands2017PhD

Vol: Pages:

Comment: The horizontal offset in the two eyes’ locations in the skull means that they receive slightly different images of the world. The visual cortex uses these disparities to calculate where in depth different objects are, absolutely (physical distance from the viewer, perceived very imprecisely) and relatively (whether one object is in front of another, perceived with great precision). For well over a century, stereoscopic 3D (S3D) technology has existed which can generate an artificial sense of depth by displaying images with slight disparities to the different retinas. S3D technology is now considerably cheaper to access in the home, but remains a niche market, partly reflecting problems with viewer experience and enjoyment of S3D. This thesis considers some of the factors that could affect viewer experience of S3D content. While S3D technology can give a vivid depth percept, it can also lead to distortions in perceived size and shape, particularly if content is viewed at the wrong distance or angle. Almost all S3D content is designed for a viewing angle perpendicular to the screen, and with a recommended viewing distance, but little is known about the viewing distance typically used for S3D, or the effect of viewing angle. Accordingly, Chapter 2 of this thesis reports a survey of members of the British public. Chapters 3 and 4 report two experiments, one designed to assess the effect of oblique viewing, and another to consider the interaction between S3D and perceived size. S3D content is expensive to generate, hence producers sometimes “fake” 3D by shifting 2D content behind the screen plane. Chapter 5 investigates viewer experience with this fake 3D, and finds it is not a viable substitute for genuine S3D while also examining whether viewers fixate on different image features when video content is viewed in S3D, as compared to 2D.

Nityananda V, Tarawneh G, Errington S, Serrano-Pedraza I, Read JCA ( 2017 )
The optomotor response of the praying mantis is driven predominantly by the central visual field

Journal of Comparative Physiology A Vol: 203 Pages: 77-87 [view on journal website] Pubmed ID : 28005254

Comment: The optomotor response has been widely used to
investigate insect sensitivity to contrast and motion. Several
studies have revealed the sensitivity of this response
to frequency and contrast, but we know less about the
spatial integration underlying this response. Specifically,
few studies have investigated how the horizontal angular
extent of stimuli influences the optomotor response. We
presented mantises with moving gratings of varying horizontal
extents at three different contrasts in the central or
peripheral regions of their visual fields. We assessed the
relative effectivity of different regions to elicit the optomotor
response and modelled the dependency of the response
on the angular extent subtended by stimuli at these different
regions. Our results show that the optomotor response
is governed by stimuli in the central visual field and not
in the periphery. The model also shows that in the central
region, the probability of response increases linearly with
increase in horizontal extent up to a saturation point. Furthermore,
the dependency of the optomotor response on the
angular extent of the stimulus is modulated by contrast. We
discuss the implications of our results for different modes
of stimulus presentation and for models of the underlying
mechanisms of motion detection in the mantis.

Yazdani P, Read JCA, Whittaker RG, Trevelyan AJ ( 2017 )
Assessment of epilepsy using noninvasive visual psychophysics tests of surround suppression

Physiological Reports Vol: 5(5) Pages: pii: e13079. doi: 10.14814/phy2.13079. [view on journal website] Pubmed ID : 28275107

Comment: Powerful endogenous inhibitory mechanisms are thought to restrict the spread of epileptic discharges in cortical networks. Similar inhibitory mechanisms also influence physiological processing. We reasoned, therefore, that useful information about the quality of inhibitory restraint in individuals with epilepsy may be gleaned from psychophysical assays of these physiological processes. We derived a psychophysical measure of cortical inhibition, the motion surround suppression index (SSI), in 54 patients with epilepsy and 146 control subjects. Multivariate regression analyses showed that SSI was predicted strongly by age and seizure type, but not by seizure frequency. Specifically, we found that patients with exclusively focal epilepsy, and no history of generalization, showed significantly stronger cortical inhibition as measured by the SSI compared to all other groups, including controls. In contrast, patients with focal seizures evolving into generalized seizures, and patients with generalized genetic epilepsy, showed similar levels of cortical inhibition to controls. The presumptive focus, when one could be identified, was rarely found in visual cortex, meaning that the relationship with the epilepsy subtype is likely to reflect some global difference in inhibition in these subjects. This is the first reported instance of raised SSI in any patient cohort, and appears to differentiate between patients with respect to the likelihood of their experiencing generalization of their seizures. These results suggest that such simple psychophysical assays may provide useful aids to clinical management, particularly at the time of diagnosis.

Vancleef K, Read JCA, Herbert W, Goodship N, Woodhouse M, Serrano-Pedraza I ( 2017 )
Overestimation of stereo thresholds by the TNO stereotest is not due to global stereopsis.

Ophthalmic and Physiological Optics Vol: 37(4) Pages: 507-520 [view on journal website] Pubmed ID : 28337792

Comment: Purpose
It has been repeatedly shown that the TNO stereotest overestimates stereo threshold compared to other clinical stereotests. In the current study, we test whether this overestimation can be attributed to a distinction between ‘global’ (or ‘cyclopean’) and ‘local’ (feature or contour-based) stereopsis.
Methods
We compared stereo thresholds of a global (TNO) and a local clinical stereotest (Randot Circles). In addition, a global and a local psychophysical stereotest were added to the design. One hundred and forty-nine children between 4 and 16 years old were included in the study.
Results
Stereo threshold estimates with TNO were a factor of two higher than with any of the other stereotests. No significant differences were found between the other tests. Bland-Altman analyses also indicated low agreement between TNO and the other stereotests, especially for higher stereo threshold estimates. Simulations indicated that the TNO test protocol and test disparities can account for part of this effect.
Discussion
The results indicate that the global – local distinction is an unlikely explanation for the overestimated thresholds of TNO. Test protocol and disparities are one contributing factor. Potential additional factors include the nature of the task (TNO requires depth discrimination rather than detection) and the use of anaglyph red/green 3D glasses rather than polarizing filters, which may reduce binocular fusion.

Hands P, Read JCA ( 2017 )
True stereoscopic 3D cannot be simulated by shifting 2D content off the screen plane

Displays Vol: 48 Pages: 35-40 [view on journal website]

Comment: money by including brief sections of 2D content displayed with a uniform disparity, i.e. the 2D image is
geometrically shifted behind the screen plane. This manipulation is believed to produce an illusion of
depth which, while not as powerful as true S3D, is nevertheless more compelling than simple 2D. Our
study examined whether this belief is correct. 30 s clips from a nature documentary were shown in
the original S3D, in ordinary 2D and in shifted versions of S3D and 2D. Participants were asked to determine
the impression of depth on a 7 point Likert scale. There was a clear and highly significant difference
between the S3D depth perception (mean 6.03) and the shifted 2D depth perception (mean 4.13)
(P = 0.002, ANOVA). There was no difference between ordinary 2D presented on the screen plane, and
the shifted 2D. We conclude that the shifted 2D method not only fails to mimic the depth effect of true
S3D, it in fact has no benefit over ordinary 2D in terms of the depth illusion created. This could impact
viewing habits of people who notice the difference in depth quality.

Rosner R, von Hadeln J, Salden T, Homberg U ( 2017 )
Anatomy of the lobula complex in the brain of the praying mantis compared to the lobula complexes of the locust and cockroach

Journal of Comparative Neurology Vol: 525 (10) Pages: 2343–2357 [view on journal website] Pubmed ID : 28295329

Read JCA, Cumming BG ( 2017 )
Visual Perception: Neural Networks for Stereopsis

Current Biology Vol: 27(12) Pages: R594–R596 [view on journal website]

Comment: This is a comment article on Welchman and Goncalves (2017): ‘‘What not’’ detectors help the brain see in depth. Curr. Biol. 27, 1403–1412.

Nityananda V, Read JCA ( 2017 )
Stereopsis in animals: evolution, function and mechanisms

Journal of Experimental Biology Vol: 220 Pages: 2502-2512 [view on journal website] Pubmed ID : 28724702

Comment: Stereopsis is the computation of depth information from views
acquired simultaneously from different points in space. For many
years, stereopsis was thought to be confined to primates and other
mammals with front-facing eyes. However, stereopsis has now been
demonstrated in many other animals, including lateral-eyed prey
mammals, birds, amphibians and invertebrates. The diversity of
animals known to have stereo vision allows us to begin to investigate
ideas about its evolution and the underlying selective pressures in
different animals. It also further prompts the question of whether all
animals have evolved essentially the same algorithms to implement
stereopsis. If so, this must be the best way to do stereo vision, and
should be implemented by engineers in machine stereopsis.
Conversely, if animals have evolved a range of stereo algorithms in
response to different pressures, that could inspire novel forms of
machine stereopsis appropriate for distinct environments, tasks or
constraints. As a first step towards addressing these ideas, we here
review our current knowledge of stereo vision in animals, with a view
towards outlining common principles about the evolution, function
and mechanisms of stereo vision across the animal kingdom. We
conclude by outlining avenues for future work, including research into
possible new mechanisms of stereo vision, with implications for
machine vision and the role of stereopsis in the evolution of
camouflage.

Ushaw G, Sharp S, Hugill J, Rafiq S, Black C, Casanova T, Vancleef K, Read JCA, Morgan G ( 2017 )
Analysis of Soft Data for Mass Provision of Stereoacuity Testing Through a Serious Game for Health

Proceedings of the 2017 International Conference on Digital Health (DH '17). ACM, New York, NY, USA. Vol: 6 Pages: 216-220 [view on journal website]

DOI: https://doi.org/10.1145/3079452.307949
Comment: Mass provision of healthcare through a digital medium can be greatly enhanced by the use of serious games. The accessibility and engagement provided by a serious game to the subject can significantly increase participation. The commercial games industry employs numerous techniques to analyse soft data collected from early users of an application to evolve the application itself and improve the experience of playing it. A game for mass stereoacuity testing of young children is used as a case study in this paper, to illustrate how soft feedback can be used to improve the effectiveness of a clinical trial. The key to the approach is identified as rapid incremental evolution of the application and trial protocol in a manner which increases the amount and usefulness of soft data collected, and reacts to issues identified in the soft data in a timely fashion. It is hoped that the approach can be adopted for a wide range of digital applications for mass health provision.

Tarawneh G, Nityananda V, Rosner R, Errington S, Herbert W, Cumming BG, Read JCA, Serrano-Pedraza I ( 2017 )
Invisible noise obscures visible signal in insect motion detection

Scientific Reports Vol: 7: 3496 Pages: 1-14 [view on journal website] Pubmed ID : 28615659

Comment: The motion energy model is the standard account of motion detection in animals from beetles to
humans. Despite this common basis, we show here that a difference in the early stages of visual
processing between mammals and insects leads this model to make radically different behavioural
predictions. In insects, early filtering is spatially lowpass, which makes the surprising prediction that
motion detection can be impaired by “invisible” noise, i.e. noise at a spatial frequency that elicits
no response when presented on its own as a signal. We confirm this prediction using the optomotor
response of praying mantis Sphodromantis lineola. This does not occur in mammals, where spatially
bandpass early filtering means that linear systems techniques, such as deriving channel sensitivity from
masking functions, remain approximately valid. Counter-intuitive effects such as masking by invisible
noise may occur in neural circuits wherever a nonlinearity is followed by a difference operation.

Peterzell DH, Serrano-Pedraza I, Widdall M, Read JCA ( 2017 )
Thresholds for sine-wave corrugations defined by binocular disparity in random dot stereograms: Factor analysis of individual differences reveals two stereoscopic mechanisms tuned for spatial frequency

Vision Research Vol: 141 Pages: 127-135 [view on journal website] Pubmed ID : 29155009

Read JCA, Godfrey A, Bohr I, SImonotto J, Galna B, Smulders TV ( 2016 )
Viewing 3D TV over two months produces no discernible effects on balance, coordination or eyesight.

Ergonomics Vol: Jan 13 Pages: 1-16 [view on journal website] Pubmed ID : 26758965

Comment: With the rise in stereoscopic 3D media, there has been concern that viewing stereoscopic 3D (S3D) content could have long-term adverse effects, but little data are available. In the first study to address this, 28 households who did not currently own a 3D TV were given a new TV set, either S3D or 2D. The 116 members of these households all underwent tests of balance, coordination and eyesight, both before they received their new TV set, and after they had owned it for 2 months. We did not detect any changes which appeared to be associated with viewing 3D TV. We conclude that viewing 3D TV does not produce detectable effects on balance, coordination or eyesight over the timescale studied. Practitioner Summary: Concern has been expressed over possible long-term effects of stereoscopic 3D (S3D). We looked for any changes in vision, balance and coordination associated with normal home S3D TV viewing in the 2 months after first acquiring a 3D TV. We find no evidence of any changes over this timescale.

Nityananda V, Tarawneh G, Rosner R, Nicolas J, Crichton S, Read JCA ( 2016 )
Insect stereopsis demonstrated using a 3D insect cinema

Scientific Reports Vol: 6 Pages: 18718 [view on journal website] Pubmed ID : 26740144

Newcastle University press release. Video clips from Tyne Tees news. New York Times. LA Times. HuffPo. Sky News. The Independent. Daily Mail. Wissenschaft. El Correo. Metronews France.
Comment: Stereopsis - 3D vision – has become widely used as a model of perception. However, all our knowledge of possible underlying mechanisms comes almost exclusively from vertebrates. While stereopsis has been demonstrated for one invertebrate, the praying mantis, a lack of techniques to probe invertebrate stereopsis has prevented any further progress for three decades. We therefore developed a stereoscopic display system for insects, using miniature 3D glasses to present separate images to each eye, and tested our ability to deliver stereoscopic illusions to praying mantises. We find that while filtering by circular polarization failed due to excessive crosstalk, “anaglyph” filtering by spectral content clearly succeeded in giving the mantis the illusion of 3D depth. We thus definitively demonstrate stereopsis in mantises and also demonstrate that the anaglyph technique can be effectively used to deliver virtual 3D stimuli to insects. This method opens up broad avenues of research into the parallel evolution of stereoscopic computations and possible new algorithms for depth perception.

Nityananda V, Bissianna G, Tarawneh G, Read JCA ( 2016 )
Small or far away? Size and distance perception in the praying mantis.

Philosophical Transactions B Vol: 371(1697) Pages: pii: 20150262 [view on journal website] Pubmed ID : 27269605

Comment: Stereo or '3D' vision is an important but costly process seen in several evolutionarily distinct lineages including primates, birds and insects. Many selective advantages could have led to the evolution of stereo vision, including range finding, camouflage breaking and estimation of object size. In this paper, we investigate the possibility that stereo vision enables praying mantises to estimate the size of prey by using a combination of disparity cues and angular size cues. We used a recently developed insect 3D cinema paradigm to present mantises with virtual prey having differing disparity and angular size cues. We predicted that if they were able to use these cues to gauge the absolute size of objects, we should see evidence for size constancy where they would strike preferentially at prey of a particular physical size, across a range of simulated distances. We found that mantises struck most often when disparity cues implied a prey distance of 2.5 cm; increasing the implied distance caused a significant reduction in the number of strikes. We, however, found no evidence for size constancy. There was a significant interaction effect of the simulated distance and angular size on the number of strikes made by the mantis but this was not in the direction predicted by size constancy. This indicates that mantises do not use their stereo vision to estimate object size. We conclude that other selective advantages, not size constancy, have driven the evolution of stereo vision in the praying mantis.This article is part of the themed issue 'Vision in our three-dimensional world'.

Serrano-Pedraza I, Herbert W, Villa-Laso L, Widdall M, Vancleef K, Read JCA ( 2016 )
The stereoscopic anisotropy develops during childhood.

Investigative Ophthalmology and Visual Science Vol: 57(3) Pages: 960-70 [view on journal website] Pubmed ID : 26962692

Comment: PURPOSE:
Human vision has a puzzling stereoscopic anisotropy: horizontal depth corrugations are easier to detect than vertical depth corrugations. To date, little is known about the function or the underlying mechanism responsible for this anisotropy. Here, we aim to find out whether this anisotropy is independent of age. To answer this, we compare detection thresholds for horizontal and vertical depth corrugations as a function of age.
METHODS:
The depth corrugations were defined solely by the horizontal disparity of random dot patterns. The disparities depicted a horizontal or vertical sinusoidal depth corrugation of spatial frequency 0.1 cyc/deg. Detection thresholds were obtained using Bayesian adaptive staircases from a total of 159 subjects aged from 3 to 73 years. For each participant we computed the anisotropy index, defined as the log10-ratio of the detection threshold for vertical corrugations divided by that for horizontal.
RESULTS:
Anisotropy index was highly variable between individuals but was positive in 87% of the participants. There was a significant correlation between anisotropy index and log-age (r = 0.21, P = 0.008) mainly driven by a significant difference between children and adults. In 67 children aged 3 to 13 years, the mean anisotropy index was 0.34 ± 0.38 (mean ± SD, meaning that vertical thresholds were on average 2.2 times the horizontal ones), compared with 0.59 ± 0.55 in 84 adults aged 18 to 73 years (vertical 3.9 times horizontal). This was mainly driven by a decline in the sensitivity to vertical corrugations. Children had poorer stereoacuity than adults, but had similar sensitivity to adults for horizontal corrugations and were actually more sensitive than adults to vertical corrugations.
CONCLUSIONS:
The fact that adults show stronger stereo anisotropy than children raises the possibility that visual experience plays a critical role in developing and strengthening the stereo anisotropy.

Henriksen S, Cumming BG, Read JCA ( 2016 )
A single mechanism can account for human perception of depth in mixed correlation random dot stereograms

PLOS Computational Biology Vol: 12(5) Pages: e1004906:1-21 [view on journal website]

All simulations were implemented in Sid Henriksen's BEMtoolbox: a custom Matlab toolbox for simulating binocular neurons. The toolbox is available at http://github.com/sidh0/BEMtoolbox. All code used in the current manuscript is available online at http://github.com/sidh0/hcr16_ploscb (requires BEMtoolbox).
Comment: Relating neural activity to perception is one of the most challenging tasks in neuroscience.
Stereopsis—the ability of many animals to see in stereoscopic 3D—is a particularly tractable
problem because the computational and geometric challenges faced by the brain are
very well understood. In essence, the brain has to work out which elements in the left eye’s
image correspond to which in the right image. This process is believed to begin in primary
visual cortex (V1). It has long been believed that neurons in V1 achieve this by computing
the correlation between small patches of each eye’s image. However, recent psychophysical
experiments have reported depth perception in stimuli for which this correlation is zero,
suggesting that another mechanism might be responsible for matching the left and right
images in this case. In this article, we show how a simple modification to model neurons
that compute correlation can account for depth perception in these stimuli. Our model
cells mimic the response properties of real cells in the primate brain, and importantly, we
show that a perceptual decision model that uses these cells as its basic elements can capture
the performance of human observers on a series of visual tasks. That is, our computer
model of a brain area, based on experimental data about real neurons and using only a single
type of depth computation, successfully explains and predicts human depth judgments
in novel stimuli. This reconciles the properties of human depth perception with the properties
of neurons in V1, bringing us closer to understanding how neuronal activity causes
perception.

Henriksen S, Read JCA, Cumming BG ( 2016 )
Neurons in Striate Cortex Signal Disparity in Half-Matched Random-Dot Stereograms

Journal of Neuroscience Vol: 36(34) Pages: 8967– 8976 [view on journal website] Pubmed ID : 27559177

Comment: Human stereopsis can operate in dense “cyclopean” images containing no monocular objects. This is believed to depend on the computation of binocular correlation by neurons in primary visual cortex (V1). The observation that humans perceive depth in half-matched random-dot stereograms, although these stimuli have no net correlation, has led to the proposition that human depth perception in these stimuli depends on a distinct “matching” computation possibly performed in extrastriate cortex. However, recording from disparity-selective neurons in V1 of fixating monkeys, we found that they are in fact able to signal disparity in half-matched stimuli. We present a simple model that explains these results. This reinstates the view that disparity-selective neurons in V1 provide the initial substrate for perception in dense cyclopean stimuli, and strongly suggests that separate correlation and matching computations are not necessary to explain existing data on mixed correlation stereograms.

Serrano-Pedraza I, Vancleef K, Read JCA ( 2016 )
Avoiding monocular artifacts in clinical stereotests presented on column-interleaved digital stereoscopic displays

Journal of Vision Vol: 16(14):13 Pages: 1-14 [view on journal website] Pubmed ID : 27846341

Comment: New forms of stereoscopic 3-D technology offer vision
scientists new opportunities for research, but also
come with distinct problems. Here we consider
autostereo displays where the two eyes’ images are
spatially interleaved in alternating columns of pixels
and no glasses or special optics are required. Columninterleaved
displays produce an excellent stereoscopic
effect, but subtle changes in the angle of view can
increase cross talk or even interchange the left and
right eyes’ images. This creates several challenges to
the presentation of cyclopean stereograms (containing
structure which is only detectable by binocular vision).
We discuss the potential artifacts, including one that is
unique to column-interleaved displays, whereby scene
elements such as dots in a random-dot stereogram
appear wider or narrower depending on the sign of
their disparity. We derive an algorithm for creating
stimuli which are free from this artifact.We show that
this and other artifacts can be avoided by (a) using a
task which is robust to disparity-sign inversion—for
example, a disparity-detection rather than
discrimination task—(b) using our proposed algorithm
to ensure that parallax is applied symmetrically on the
column-interleaved display, and (c) using a dynamic
stimulus to avoid monocular artifacts from motion
parallax. In order to test our recommendations, we
performed two experiments using a stereoacuity task
implemented with a parallax-barrier tablet. Our
results confirm that these recommendations eliminate
the artifacts. We believe that these recommendations
will be useful to vision scientists interested in running
stereo psychophysics experiments using parallaxbarrier
and other column-interleaved digital displays

O'Hanlon, CG and Read JCA ( 2016 )
Blindness to background: an inbuilt bias for visual objects

Developmental Science Vol: DOI: 10.1111/desc.12478 Pages: 1-23 [view on journal website] Pubmed ID : 27873433

A video abstract describing the main findings. Here is a press release by Aberystwyth University. Our complete Matlab code for these experiments, including the code for operating the RED50 eye tracker, is available here ExptRED.zip. See also here.
Comment: Sixty-eight 2- to 12-year-olds and 30 adults were shown colorful displays on a touchscreen monitor and trained to point to the location of a named color. Participants located targets near-perfectly when presented with four abutting colored patches. When presented with three colored patches on a colored background, toddlers failed to locate targets in the background. Eye tracking demonstrated that the effect was partially mediated by a tendency not to fixate the background. However, the effect was
abolished when the targets were named as nouns, whilst the change to nouns had little impact on eye movement patterns. Our results imply a powerful, inbuilt tendency to attend to objects, which may slow the development of color concepts and acquisition of color words.

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Henriksen S, Read JCA ( 2016 )
Visual Perception: A Novel Difference Channel in Binocular Vision

Current Biology Vol: 26(12) Pages: R500–R503 [view on journal website] Pubmed ID : 27326711

This article is a commentary on May & Zhaoping 2016, "Efficient Coding Theory Predicts a Tilt Aftereffect from Viewing Untilted Patterns", Current Biology 26: 1571–1576
Comment: A "Dispatch", i.e. a comment article, about May & Zhaoping 2016 "Efficient Coding Theory Predicts a Tilt Aftereffect from Viewing Untilted Patterns". Our summary: "A recent study provides compelling evidence that binocular vision uses two separate channels; one channel adds the images from the two eyes, and the other subtracts them. "

Mazurek A, Bhoopathy R, Read JCA, Gallagher P, Smulders TV ( 2015 )
What-Where-When memory, unlike other cognitive abilities, is unimpaired in healthy people over 70

Frontiers in Aging Neuroscience Vol: 7 Pages: 00074 [view on journal website] Pubmed ID : 26042030

This paper used a Bayes Factor analysis for binomial data. The code is available here, both as Matlab code and as an executable to download.

Read JCA, Georgiou R, Brash C, Yazdani P, Whittaker R, Trevelyan A, Serrano-Pedraza I ( 2015 )
Moderate acute alcohol intoxication has minimal effect on surround suppression measured with a motion direction discrimination task

Journal of Vision Vol: 15(1):5 Pages: 1-14 [view on journal website] Pubmed ID : 25583875

Nityananda V, Tarawneh G, Jones L, Busby N, Herbert W, Davies R, Read JCA ( 2015 )
The contrast sensitivity function of the praying mantis Sphodromantis lineola

Journal of Comparative Physiology A Vol: 201(8) Pages: 741-50 [view on journal website] Pubmed ID : 25894490

Here you can find the raw data for this paper, in Matlab format, and also an Excel file reporting the fitted thresholds for the individual insects and for the aggregate data pooled across individuals, using the methods reported in the paper. Also, see this blog post on a subtlety concerning the definition of frequency.

Hands P, Khushu A, Read JCA ( 2015 )
Interaction between size and disparity cues in distance judgements

3D Imaging (IC3D), 2014 International Conference on Vol: Pages: 1-5 [view on journal website]

Read JCA ( 2015 )
What is stereoscopic vision good for?

Proc. SPIE 9391, Stereoscopic Displays and Applications XXVI, 93910N (March 17, 2015); doi:10.1117/12.2184988 Vol: Pages: [view on journal website]

Hands P, Smulders TV, Read JCA ( 2015 )
Stereoscopic 3D content appears relatively veridical when viewed from an oblique angle

Journal of Vision Vol: 15(5):6 Pages: 1-21 [view on journal website] Pubmed ID : 26067524

Comment: Geometrically, stereoscopic 3-D (S3D) content should appear distorted unless viewed from the position for which the content was produced. Almost all commercial and laboratory S3D content is generated assuming that it will be presented on a screen frontoparallel to the viewer. However, in cinema and the home, S3D content is regularly viewed from oblique angles, and yet shapes are not usually perceived to be distorted. It is not yet known whether this is simply because viewers are insensitive to incorrect viewing angles or because viewers automatically compensate for oblique viewing, as they do for 2-D content. Here, we investigate this using a canonical-form paradigm. We show that S3D content can indeed appear warped when viewed from oblique angles, and that this effect is more pronounced than for 2-D content. We hypothesized that motion cues in the content would aid in the correct perception of S3D content, making it appear more natural even when viewed obliquely, but we find little support for this idea. However, the perceptual distortions are still small, and viewers do compensate to some extent for oblique viewing. We conclude that, at least as regards object distortion, oblique viewing is unlikely to be substantially more of a problem for S3D content than it already is for 2-D.

Yazdani P, Serrano-Pedraza I, Whittaker R, Trevelyan A, Read JCA ( 2015 )
Two common psychophysical measures of surround suppression reflect independent neuronal mechanisms

Journal of Vision Vol: 15 (21) Pages: 1-14 [view on journal website] Pubmed ID : 26401628

Comment: Psychophysical surround suppression is believed to reflect inhibitory neuronal mechanisms in visual cortex. In recent years, two psychophysical measures of surround suppression have been much studied: (i) duration thresholds on a motion-discrimination task (which are worse for larger than for smaller stimuli) and (ii) contrast thresholds on a contrast-detection task (which are worse when grating stimuli are surrounded by a stimulus of the same orientation than when they are presented in isolation or surrounded by a stimulus of orthogonal orientation). Changes in both metrics have been linked to several different human conditions, including aging, differences in intelligence, and clinical disorders such as schizophrenia, depression, and autism. However, the exact nature of the neuronal correlate underlying these phenomena remains unclear. Here, we use an individual-differences approach to test the hypothesis that both measures reflect the same property of the visual system, e.g., the strength of GABA-ergic inhibition across visual cortex. Under this hypothesis we would expect the two measures to be significantly positively correlated across individuals. In fact, they are not significantly correlated. In addition, we replicate the previously reported correlation between age and motion-discrimination surround suppression, but find no correlation between age and contrast-detection surround suppression. We conclude that the two forms of psychophysical surround suppression arise independently from different cortical mechanisms.

Read JCA, Vancleef K, Serrano-Pedraza I, Morgan G, Sharp C, Clarke MP ( 2015 )
ASTEROID: Accurate STEReoacuity measurement in the eye clinic

Perception Vol: 44(S1) Pages: 75 [view on journal website]

Read JCA, Simonotto J, Bohr I, Godfrey A, Galna B, Rochester L, Smulders TV ( 2015 )
Balance and coordination after viewing stereoscopic 3D television

Royal Society Open Science Vol: 2 Pages: 140522 [view on journal website]

Data set available here.

Discussion of this paper on The Conversation website.
Comment: Manufacturers and the media have raised the possibility that viewing stereoscopic 3D television (S3D TV) may cause temporary disruption to balance and visuomotor coordination. We looked for evidence of such effects in a laboratory-based study. Four hundred and thirty-three people aged 4–82 years old carried out tests of balance and coordination before and after viewing an 80 min movie in either conventional 2D or stereoscopic 3D, while wearing two triaxial accelerometers. Accelerometry produced little evidence of any change in body motion associated with S3D TV. We found no evidence that viewing the movie in S3D causes a detectable impairment in balance or in visuomotor coordination.

Read JCA ( 2014 )
Viewer experience with stereoscopic 3D television in the home

Displays Vol: 35 Pages: 252-260 [view on journal website]

Read JCA, Bohr I ( 2014 )
User experience while viewing stereoscopic 3D television

Ergonomics Vol: 57(8) Pages: 1140-53 [view on journal website] Pubmed ID : 24874550

Journal press release "Good news for couch potatoes".

Read JCA ( 2014 )
The place of human psychophysics in modern neuroscience

Neuroscience Vol: 296 Pages: 116-29 [view on journal website] Pubmed ID : 24880153

ERRATA

Read JCA ( 2014 )
Models of stereo vision

Encyclopedia of Computational Neuroscience Vol: Springer Reference Pages: [view on journal website]

Read JCA ( 2014 )
Stereo vision and strabismus

Eye Vol: 29 Pages: 214–224 [view on journal website] Pubmed ID : 25475234

Serrano-Pedraza I, Romero-Ferreiro V, Read JCA, Diéguez-Risco T, Bagney A, Caballero-González M, Rodríguez-Torresano J, Rodriguez-Jimenez J ( 2014 )
Reduced visual surround suppression in schizophrenia shown by measuring contrast detection thresholds

Frontiers in Psychology Vol: 5 Pages: [view on journal website] Pubmed ID : 25540631

Comment: I collaborated on this study by Ignacio Serrano-Pedraza, which uses a psychophysical index of surround suppression employed in several of our previous studies. Here, a grating in the visual periphery needs higher contrast to be visible when it is surrounded by a bigger grating of the same orientation. The effect is believed to depend on inhibitory mechanisms in visual cortex. Here, we demonstrate that people with schizophrenia show relatively less suppression under this index, possibly due to differences in cortical inhibition in this group.

Tarawneh G, Read JCA ( 2014 )
An FPGA-based hardware accelerator for simulating spatiotemporal neurons

Electronics, Circuits and Systems (ICECS), 21st IEEE International Conference on Vol: 2014 Pages: 618 - 621 [view on journal website]

Comment: Simulating spatiotemporal neurons is fundamental to understanding motion detection mechanisms in the primary
visual cortex and cloning these mechanisms in digital systems. We present a hardware accelerator that leverages the parallelism
of a modern Field Programmable Gate Array (FPGA) to increase the speed of spatiotemporal computations by 12 orders of
magnitude for video framebuffer sizes up to 128×128×25 pixels. The accelerator is primarily intended for running simulations
of large spatiotemporal neuron populations but can also be used in computer vision applications that require high-speed spatiotemporal processing such as realtime motion detection.

Serrano-Pedraza I, Brash C, Read JCA ( 2013 )
Testing the horizontal-vertical stereo anisotropy with the critical-band masking paradigm

Journal of Vision Vol: 13(11):15 Pages: 1-15 [view on journal website] Pubmed ID : 24071587

Read JCA ( 2013 )
Man, mantis and machine : the computation of 3D vision

Leverhulme Trust Annual Review Vol: Pages:

Hands P, Read JCA ( 2013 )
Perceptual compensation mechanisms when viewing stereoscopic 3D from an oblique angle

International Conference on 3D Imaging (IC3D), 2013 Vol: Pages: 1 - 5 [view on journal website]

DOI = 10.1109/IC3D.2013.6732086

Bohr I, Read JCA ( 2013 )
Stereoacuity with Frisby and revised FD2 stereo tests

PLOS ONE Vol: 8(12) Pages: e82999 [view on journal website] Pubmed ID : 3861460

Read JCA, Hands P ( 2013 )
Review of James Stone's book "Vision and brain: How we perceive the world"

Perception Vol: 42(6) Pages: 685 [view on journal website]

Comment: Review of James Stone's "Vision and brain: How we perceive the world"

Read JCA, Allenmark PF ( 2013 )
Visual Perception: One World from Two Eyes

Current Biology Vol: 23(11) Pages: R483-R486 [view on journal website] Pubmed ID : 23743415

Read JCA, Begum SF, McDonald A, Trowbridge J ( 2013 )
The binocular advantage in visuomotor tasks involving tools

i-Perception Vol: 4 Pages: 101–110 [view on journal website] Pubmed ID : 23755355

Read JCA, Robson JH, Smith CL, Lucas AD ( 2012 )
The scintillating grid illusion is enhanced by binocular viewing

i-Perception Vol: 3(10) Pages: 820–830 [view on journal website] Pubmed ID : 23482297

Press release on Newcastle University website.
Comment: This paper was prompted by a question from the audience in a public lecture I gave at the Newcastle Centre for Life. I used the rather fabulous scintillating grid illusion (Schrauf, Lingelbach and Wist, 1994) as a "weird optical illusion" demo. A gentleman in the audience said ,"It doesn't scintillate so much if you cover one eye." I'd never noticed that, but did a quick show of hands, and sure enough most people seemed to agree. I had three local sixth-formers due to come to my lab to do science projects under the Nuffield summer bursary scheme, and I thought I'd have one of them look into this. Andrew Lucas went back to the Centre for Life and other public areas of Newcastle, and got people to rate the scintillations while wearing glasses which allowed them to see out of one or both eyes. He too got the same effect, which was interesting as it hadn't been reported in the existing literature. Before I published it, I wanted to collect more formal data, so I set up an experiment on a 3D monitor, which allowed me to interleave binocular and monocular images, without participants even noticing. Two undergraduates, Chris Smith and Joe Robson, ran these experiments as their third-year project. It was fun to run a project which had so many non-professional scientists contributing.

Vuong QC, Friedman A, Read JCA ( 2012 )
The relative weight of shape and non-rigid motion cues in object perception: A model of the parameters underlying dynamic object discrimination

Journal of Vision Vol: 12(3): 16 Pages: 1-20 [view on journal website] Pubmed ID : 22427696

Comment: This is a paper with my colleague Quoc and his collaborator Alinda over in Canada. Once again, my contribution is a tedious appendix filled with equations. Quoc and Alinda were interested in how much we recognise objects by their shape, and how much by their characteristic motion. We’ve probably all had the experience of recognising a friend from behind by their gait, for example. Quoc and Alinda came up with cool stimuli which could be differentiated either by their shape, or by their movement, or both. I helped develop a cue-combination model to quantify how much weight people were giving to each cue.

Brilot BO, Bateson M, Nettle N, Whittingham MJ, Read JCA ( 2012 )
When is general wariness favored in avoiding multiple predator types?

American Naturalist Vol: 179(6) Pages: E180-E195 [view on journal website] Pubmed ID : 22617270

Comment: I’m fond of this paper because it's my first ecology paper. If you've been reading this far, you know that I'm all about stereo vision - its properties, neuronal basis, cortical location and so on. This paper, in contrast, is about predator-prey relations, e.g. a sparrow trying to avoid being eaten by a cat or a hawk. Needless to say, the ecology in this paper comes from the other authors. My contribution was to help with the mathematical modelling. Ben Brilot, the first author, and his PI Melissa Bateson (another Royal Society University Research Fellow before she became a Reader here at Newcastle), are interested in anxiety and wariness in animals. In this project, they and our colleagues Daniel Nettle and Mark Whittingham were interested specifically in how a prey animal's optimal behaviour changes if it has to avoid not one, but two or more predators which place conflicting demands on the animal. If the overall danger level rises, should the animal simply become more wary to every potential threat, or should it target its wariness towards the greater danger? We thought that signal detection theory could be a useful framework, and Ben and I spent a lot of time sitting down together trying to figure out how to make that work. As ever, the issue was how to simplify the problem enough to make progress while still retaining enough complexity to make it interesting. I think we both found it a really interesting experience. I was fascinated to get this insight into my ecological colleagues' field, and blown away by the depth and breadth of their knowledge across so many species and situations.

Banks MS, Read JCA, Allison RS, Watt SJ ( 2012 )
Stereoscopy and the Human Visual System

Motion Imaging Vol: 121 (4) Pages: 24-43 [view on journal website] Pubmed ID : 23144596

This paper was cited by the Society of Motion Picture and Television Engineers for a Certificate of Merit as an outstanding paper published in Motion Imaging during 2012.
Comment: In July 2011, the Society of Motion Picture and Television Engineers (SMPTE) held its 2nd International Conference on Stereoscopic 3D for Media & Entertainment in New York. Marty Banks from Berkeley, Rob Allison from York University in Toronto, Simon Watts from Bangor and I jointly presented a seminar on stereoscopy and the human visual system. The aim was to lay out some of the key findings from vision science which relate to the design of 3D displays including 3D TV and cinema. We collaborated closely on our presentations, and afterwards wrote them up together into this paper.

Serrano-Pedraza I, Grady J, Read JCA ( 2012 )
Spatial frequency bandwidth of surround suppression tuning curves

Journal of Vision Vol: 12(6):24 Pages: 1-11 [view on journal website] Pubmed ID : 22715195

Allenmark PF, Read JCA ( 2012 )
Conjunctions between motion and disparity are encoded with the same spatial resolution as disparity alone

Journal of Neuroscience Vol: 32(41) Pages: 14331–14343 [view on journal website] Pubmed ID : 23055504

Comment: This paper, sadly my last with my talented PhD student Fredrik, is another example of how rubbish my intuition is! As you'll see from Fredrik's other papers, we'd been thinking a lot about how the neuronal encoding of disparity places limits on our spatial resolution, drawing inspiration from the pair of 2004 papers from my former colleagues Bruce and Hendrikje, and from Marty Banks, Mike Landy and Serge Gepshtein (whom Fredrik visited at RIKEN). It was now looking pretty convincing that human spatial resolution for disparity is set by the receptive fields of V1 neurons. Fredrik and I wondered if we could detect the psychophysical signature of other cortical areas in the same way. Area MT contains many neurons which can detect conjunctions between disparity and motion, but these neurons have much larger receptive fields than those in V1. We devised a task which required humans to do just that. It's a harder task than just detecting disparity, but we equalised the difficulty by varying the coherence of the stimulus. I was convinced that people would have even worse spatial resolution for this task than for disparity, reflecting the larger receptive fields in MT. In fact, resolution was only slightly worse than for disparity, nowhere near as coarse as it would have been if MT receptive field size were limiting resolution. I found this surprising and interesting. Yes, the initial disparity/motion information is encoded by V1, but we would expect that information to be "read out" in some other brain area, and at the moment it's not clear where that is. In fact, if I'd thought about things more, I might not have been so surprised. The spatial resolution for motion (on its own, not in conjunction with disparity) is already too good to be explained by MT receptive fields. fMRI suggests some candidate areas, but as far as I'm aware, no one has yet recorded from neurons with properties that seem able to explain our good resolution for motion, disparity and the conjunctions between them.

Read JCA ( 2012 )
Understanding visual cues to depth

Current Biology Vol: 22 (5) Pages: R163-R165 [view on journal website] Pubmed ID : 22401898

Comment on Curr Biol. 2012 Mar 6;22(5):426-31.
Comment: This is a "Dispatch" article commenting on a cool paper by Robert Held, Emily Cooper and Marty Banks in the same issue of Current Biology, "Blur and Disparity are Complementary Cues to Depth."

Read JCA, Vaz X, Serrano-Pedraza I ( 2011 )
Independent mechanisms for bright and dark image features in a stereo correspondence task

Journal of Vision Vol: 11(12):4 Pages: 1-14 [view on journal website] Pubmed ID : 21984818

Comment: I've long been intrigued by the 1995 Nature paper by Julie Harris and Andrew Parker, where they show that people perform better on a disparity task when the stimulus uses white and black dots on a grey background, than when the dots are all white or all black. They explain the effect by arguing that the stereo correspondence problem - that is, matching up which features in the two eyes correspond to the same object in space - is easier with black and white dots. Mixed colours instantly halves the complexity of the problem, because you know that a black dot can't match with a white dot. That does sound very reasonable, but my problem is that I come at stereo correspondence from the perspective of the energy model, which effectively implements cross-correlation between the two eyes' images. Cross-correlation doesn't "see" dots at all. I couldn't figure out how to implement Julie and Andrew's explanation using current models of cells in early visual cortex.
I did, however, think I could see a way round the problem. Julie and Andrew's paper started with an easy stereo task - seeing which of two adjacent planes was closer. The planes were defined by dots which were randomly scattered in X and Y, but all at the same Z (where the Z axis defines distance from the observer). They then made the task harder by introducing disparity noise, i.e. giving each dot some jitter in Z. This meant you had to average over several dots in order to get a good estimate of mean Z.
When I coded up this stimulus and had a look at it, it immediately struck me that it didn't noticeably challenge stereo correspondence. I felt I could clearly see each dot in space, indicating that my brain had successfully solved the correspondence problem. But the task was hard, because it wasn't obvious which cloud of dots was closer. Once I'd realised that, I thought I might have a way out of my difficulty. Stereo correspondence would proceed by, essentially, cross-correlation, and mixed black/white dots would offer no advantage over all-white and all-black dots. But then, in order to do Julie and Andrew's task, a higher brain area would have to figure out which dots to average over. Maybe that brain area is only able to average over a certain number of dots within each category, and therefore adding a different category ("black" as well as "white") improves performance. So when Xavier Vaz, a Biomedical Sciences undergraduate, did his project in my lab, I had him test this theory by comparing Julie and Andrew's original task with a different one designed to challenge stereo correspondence, but to be trivial once correspondence had been achieved. I was confident the mixed-colour advantage would show up on the original task and be abolished in our new experiment.
And I was completely wrong. Performance on both tasks was clearly better for mixed black-and-white dots. Julie and Andrew's result holds not only in their original task, but also in this new version of it. And I still don't have a clue how to reconcile this with my understanding of how disparity is encoded in early visual cortex.

Allenmark PF, Read JCA ( 2011 )
Spatial stereoresolution for depth corrugations may be set in primary visual cortex

PLoS Computational Biology Vol: 7(8) Pages: e1002142 [view on journal website] Pubmed ID : PMC3158043

Comment: We weren't sure at first how much of a problem this was for the existing model. In principle, it could require fundamental changes, for example indicating that stereoresolution is set at a much higher cortical level than V1. However, we thought of one pretty minor tweak which could potentially reconcile the model and data. V1 neurons are believed to show a "size-disparity correlation", i.e. the larger disparities are encoded by neurons with larger receptive fields. In our model, a single "correlation detector" represents a pool of V1 neurons tuned to different spatial frequencies and orientations. The size of the window within which interocular correlation is computed represents the minimum receptive field of neurons in this pool. In our previous model, following Gepshtein, Banks, Landy et al, we had assumed that this window was the same for all disparities. Now, we made the window larger for neuronal pools tuned to larger disparities. Now, as the amplitude of a corrugation increased, the receptive-field size of the cells encoding it also increased, limiting the ability to perceive high-frequency corrugations. It turned out that this impaired the model's ability to "see" square-wave corrugations, bringing performance down to the level of sine-waves, just as in humans.

Serrano-Pedraza I, Hogg EL, Read JCA ( 2011 )
Spatial non-homogeneity of the antagonistic surround in motion perception

Journal of Vision Vol: 11(2):3 Pages: 1–9 [view on journal website] Pubmed ID : 21292831

Serrano-Pedraza I, Manjunath V, Osunkunle O, Clarke MP, Read JCA ( 2011 )
Visual suppression in intermittent exotropia during binocular alignment

Investigative Ophthalmology and Vision Science Vol: 52(5) Pages: 2352-2364 [view on journal website] Pubmed ID : 21220559

This paper won the 2011 Pfizer Research Prize for excellent ophthalmological research in the North East.
Comment: This is my first clinical paper. Shortly after I arrived in Newcastle, Anya Hurlbert, our Institute director, put me in touch with Mike Clarke, a consultant ophthalmologist specialising in disorders of binocular vision. She figured that we’d have plenty to talk about and she was (as usual) quite right. Mike introduced me to a condition called intermittent exotropia. It’s a form of squint where the eye deviates outwards only occasionally, mainly when the person is tired and/or looking at faraway objects. What intrigued me about it was to learn that people with this condition generally retain their stereo 3D vision, the “gold standard” of binocular function, indicating that both their eyes can see well individually and can work together. And yet when their eyes are pointing in different directions, they don’t generally report any double vision, implying that input from one of the eyes has been temporarily turned off. Ignacio and I were intrigued that the brain can learn to turn the eyes’ input on and off in this way. We wondered what triggered the switch. Was it the eye movement itself, or was it the resulting change in retinal input – the fact that the two eyes’ images no longer matched up? Ignacio came up with a cool experiment to answer that question, and we spent a lot of time fine-tuning it to make it fun and enjoyable for child participants. For example, instead of dots or lines, we used child-friendly faces, such as Igglepiggle shown in the icon.
The experiment worked really well and we got a nice clear answer to our question. It turns out that eye movements are not required; it’s the retinal input which triggers the switch. If you grow up with intermittent exotropia, then your brain learns to look out for big offsets between the retinal images. That probably means that one of your eyes has turned outwards, and to avoid being troubled by double vision, your brain apparently switches to monocular mode.

Serrano-Pedraza I, Clarke MP, Read JCA ( 2011 )
Single vision during ocular deviation in intermittent exotropia

Ophthalmic and Physiological Optics Vol: 31 Pages: 45-55 [view on journal website] Pubmed ID : 21158884

Comment: Around this time Ignacio, Mike and I had been thinking a lot about intermittent exotropia as we worked on our IOVS paper, so we took this opportunity to write a little review on the subject.

Phillipson GP, Read JCA ( 2010 )
Stereo correspondence is optimized for large viewing distances

European Journal of Neuroscience Vol: doi:10.1111/j. Pages: 1460-9568.2010.07454.x. Pubmed ID : 20955471

ERRATA Comment: This paper represents Graeme's main PhD project. Graeme was interested in how stereo vision copes with the changing epipolar geometry caused by eye movements. By cleverly manipulating the geometry of the viewed stimuli, Graeme showed that stereo correspondence does not take account of changes in vertical disparity which occur as our eyes move from viewing near to far objects, but remains optimised for far viewing. I think this is a unique situation where a pattern of vertical disparity produces no depth percept on its own, but enhances the visibility of depth due to horizontal disparity.

Serrano-Pedraza I, Phillipson GP, Read JCA ( 2010 )
A specialization for vertical disparity discontinuities

Journal of Vision Vol: 10(3):2 Pages: 1-25 [view on journal website] Pubmed ID : 20377279

Comment: One of the first things I wanted to know about vertical disparity was how finely we are able to resolve it. This had been studied in a previous paper by Kaneko & Howard (1997, Vision Research 37 (20): 2871-2878), but there were a number of issues which made me feel the question hadn't been fully resolved. We used essentially the same stimulus as Kaneko & Howard: that is, an alternating version of Ogle's induced effect, in which vertical magnification alternated in strips across the image. We assumed that the task would be easiest when the magnification was constant across the whole image, and become progressively harder as the strip-width was reduced. To our surprise, this wasn't the case for most subjects. About a third of our observers did behave in this way, but most of us found that the abrupt switches in the sign of vertical magnification were quite salient and actually helped us do the task -- resulting in a band-pass, rather than a low-pass, performance profile. I have worried a lot about whether this result could be due to some artefact, but we've tested for everything we can think of and it keeps showing up time after time. So, there must be mechanisms in the brain which respond to discontinuities in vertical disparity. The existing literature emphasises the continuity of vertical disparity in natural viewing. But actually, discontinuities can occur under some circumstances, so it is possible that we have developed detectors for these.

Hardingham N, Read JCA, Trevelyan A, Nelson C, Jack JJB, Bannister N ( 2010 )
Quantal analysis reveals a functional correlation between pre- and postsynaptic efficacy from excitatory connections in rat neocortex

Journal of Neuroscience Vol: 30(4) Pages: 1441-51 [view on journal website] Pubmed ID : 20107071

Matlab code for quantal analysis

Read JCA ( 2010 )
Vertical binocular disparity is encoded implicitly within a model neuronal population tuned to horizontal disparity and orientation

PLoS Computational Biology Vol: 6(4) Pages: e1000754 [view on journal website]

Comment: In 2006, Bruce and I had suggested that the vertical disparity could exert its effects on perception via reducing the effective interocular correlation, rather than being detected and encoded directly. As explained above, we subsequently tested and disproved this idea. However, I now realised that a more sophisticated version of the same basic idea was still viable. In this paper, I simulated the activity of neurons tuned to purely horizontal disparity, and showed that they actually also encode both the magnitude and the sign of vertical disparity. This model is consistent with all psychophysics that I know of. In fact because it works so well, as far as I can see it doesn't predict any characteristic errors of perception and so can't be falsified by psychophysics. I'm currently waiting for the physiologists to tell us whether we do have neurons tuned to a range of vertical disparities at each point in the retina.

Allenmark PF, Read JCA ( 2010 )
Detectability of sine- versus square-wave disparity gratings: a challenge for current models of depth perception

Journal of Vision Vol: 10(8):17 Pages: 1-16 [view on journal website] Pubmed ID : 20884592

Comment: In 2010, my PhD student Fredrik Allenmark, my post-doctoral associate Ignacio Serrano-Pedraza and I were all thinking a lot about disparity gratings. By "gratings" here, what we mean are surfaces which are corrugated in depth, as in the two icons here. "Sine-wave gratings" are surfaces in which the corrugations are smooth waves, rather like corrugated iron, whereas "square-wave gratings" have square edges. As the corrugations get higher in frequency (i.e. up-and-down bits get closer together), it gets harder to see that the surface has this structure. "Luminance gratings", i.e. patterns of black and white stripes, have made a huge contribution to our understanding of vision. Disparity gratings have also been studied, but less extensively. We were interested in what our perception of such structures can tell us about human vision.

For his PhD project, Fredrik started with a couple of recent observations from Bruce Cumming's lab at NIH and Marty Banks' lab at Berkeley. In a linked pair of papers in The Journal of Neuroscience, these workers had shown that V1 neurons seem to respond best to frontoparallel surfaces, and had proposed that the limit of human stereoresolution -- that is, the highest-frequency gratings we can detect - is set by the size of these neurons' receptive fields. We reasoned that if this model is correct, it should be easier for us to detect square-wave gratings than sine-wave gratings. Square-wave gratings are made up of piecewise frontoparallel surfaces, to which V1 neurons respond optimally, whereas sine-wave gratings are always slanting towards or away from the observer. Fredrik first ran simulations to confirm that the model behaved as we expected, and then carried out careful experiments to see what humans perceived. To our surprise, Fredrik found that there was no difference in stereoresolution for square-wave versus sine-wave gratings. As the amplitude of high-frequency gratings increased, human performance fell to chance at the same rate for both sine-wave and square-wave gratings, whereas the model predicted that this should happen only for sine-waves.

Read JCA, Phillipson GP, Serrano-Pedraza I, Milner AD, Parker AJ ( 2010 )
Stereoscopic vision in the absence of the lateral occipital cortex

PLoS ONE Vol: 5(9) Pages: e12608 [view on journal website] Pubmed ID : 20830303

Supplementary file S1.
Supplementary file S2.
Supplementary file S3.
Comment: "D.F." is a famous neuropsychological patient who experienced carbon monoxide poisoning in an accident many years ago. This left her with long-term damage to a number of different brain areas, visible on magnetic resonance imaging. As a consequence, she has a remarkably specific visual impairment known as visual form agnosia. Although she can see colours and movement, and she can navigate the world visually without bumping into things, she cannot recognise objects visually. This is not because her vision is blurred; she has good acuity. She simply perceives objects as a meaningless jumble of elements. Fortunately for science, DF is a highly intelligent woman who is interested in her unusual brain injury, and over the past three decades she has devoted untold hours of her time to working with psychologists in order to map out the precise nature of her visual impairment. David Milner, emeritus professor at Durham, has worked extensively with DF along with his long-time colleague Mel Goodale. I highly recommend their two books, "The visual world in action" (the longer and more detailed) and "Sight Unseen" (slimmer and accessible for lay readers). On this project, I collaborated with David and with Andrew Parker from Oxford, along with my postdoc Ignacio Serrano-Pedraza and PhD student Graeme Phillipson, in order to examine DF's stereo vision.

It was already known that DF retained stereo vision, but that her stereoacuity was somewhat impaired. Standard clinical measures of stereo vision ask subjects to use stereo disparity to tell which of two surfaces was the closer. People with normal vision are incredibly precise on making such relative disparity judgments. DF could do the task, but only when the separation between the two surfaces was relatively large. Andrew had recently written a very insightful review on the neuronal basis of stereo vision in Nature Neuroscience. Based on the physiological and imaging literature Andrew reviewed, and the location of DF's most severe cortical damage, we were not surprised that DF was impaired on standard relative disparity tasks, but predicted that she would not be impaired on an absolute disparity task, i.e. judging the depth of an isolated object.

To our delight, this prediction was initially borne out. On DF's first two visits, she performed as well as age-matched controls on an absolute disparity task, but whereas they performed much better when a reference surface converted the task to a relative-disparity task, DF did not. However, this initially clean story was complicated when, after testing DF on a variety of other stimuli, she subsequently improved on the relative disparity task. It was as if we had provided training which enabled her to use information she had previously been blind to. For example, maybe her attention was not automatically drawn to the boundary demarcating the two surfaces, as controls' is, but with training she learnt where the informative region of the stimulus was. However, our results did show clearly that there is a big difference between relative disparity between adjacent surfaces (which was compromised by DF's cortical lesion) and relative disparity between transparent surfaces in relative (which DF sees perfectly). This neuropsychological evidence agrees with the predictions from physiology.

This was my first neuropsychological study, and it was a very interesting experience for me. While it is inevitably difficult working in an "n=1" situation, I found it fascinating gaining insight into DF's visual world, seeing first-hand the problems faced by someone who has a completely unique visual experience and thus no words to communicate it. I would like to record my gratitude to DF for bearing with me so patiently!

Read JCA, Phillipson GP, Serrano-Pedraza I, Milner AD, Parker AJ ( 2010 )
Stereoscopic vision in the absence of the lateral occipital cortex (Supplementary File 1)

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Read JCA, Phillipson GP, Serrano-Pedraza I, Milner AD, Parker AJ ( 2010 )
Stereoscopic vision in the absence of the lateral occipital cortex (Supplementary File 2)

Vol: Pages:

Read JCA, Phillipson GP, Serrano-Pedraza I, Milner AD, Parker AJ ( 2010 )
Stereoscopic vision in the absence of the lateral occipital cortex (Supplementary File 3)

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Serrano-Pedraza I, Read JCA ( 2010 )
Multiple channels for horizontal, but only one for vertical corrugations? A new look at the stereo anisotropy

Journal of Vision Vol: 10(12):10 Pages: 1–11 [view on journal website] Pubmed ID : 21047742

Comment: While Fredrik was measuring the high-frequency limit of our ability to perceive sine- and square-wave depth corrugations, Ignacio got interested in another aspect of sine- versus square-wave corrugations. For sine-wave corrugations, Brian Rogers and Mark Bradshaw had shown that at low frequencies, horizontal corrugations were easier to detect than vertical corrugations: that is, the corrugations didn't have to be so deep in order to be visible. At high frequencies, this difference becomes weaker. This result has been replicated in many different tasks, and represents a fundamental anisotropy of stereo vision. Ignacio showed that, at low frequencies, this anisotropy is not as strong with square-wave gratings as with sine-waves: low-frequency square-waves are about equally visible whether they are horizontal or vertical. To understand why this is, Ignacio considered two different models. In one model, the waveform is analysed as a whole, and it is detected if its RMS amplitude exceeds some threshold. In the other model, the waveform is analysed in separate frequency channels, assumed to have a bandwidth narrow enough that harmonics differing by 1.5 octaves activate separate channels. The grating is detected if the Fourier amplitude of any harmonic exceeds the threshold for that frequency, which we measure using sine-wave gratings. For vertical gratings, both models worked equally well, but for horizontal gratings, only the separate-channel model can capture the improved performance at low frequencies. One plausible interpretation of these results is that there is only a single channel available to detect vertical gratings, but there are a few (three, say) for horizontal gratings. This recasts the well-known stereo anisotropy in Fourier language: horizontal gratings are more visible at low frequencies because they activate a channel dedicated to these low frequencies, whereas vertical gratings are only perceived when their amplitude is large enough to activate the all-purpose channel, which is centered on intermediate frequencies. Obviously, more work is needed to test this hypothesis, and we intend to pursue this in the future, for example with a masking technique.

Serrano-Pedraza I, Read JCA ( 2009 )
Stereo vision requires an explicit encoding of vertical disparity

Journal of Vision Vol: 9(4):3 Pages: 1--13 [view on journal website] Pubmed ID : 19757912

Comment: This work was testing Read & Cumming (2006), where we suggested that the brain could potentially deduce vertical disparity information from the pattern of (de)correlation across the visual field, without necessarily using cells tuned to a range of vertical disparities. In this paper, we tried to construct a stimulus for which this strategy would fail. We found that perception carried on just the same, thus shooting down the model of Read & Cumming (2006) in its present form.

Bredfeldt CE, Read JCA , Cumming BG ( 2009 )
A quantitative explanation of responses to disparity defined edges in macaque V2.

Journal of Neurophysiology Vol: 101 Pages: 701-713 [view on journal website]

Comment: Christine and Bruce, the first and last authors, have a previous paper on Cyclopean Edge Responses in Macaque V2 (J Neurosci, 2006, 26:7581-7596 ) , showing that many V2 cells respond to depth edges in random-dot stereograms. They suggested there that the responses they observed could result from a simple feedforward scheme in which V2 neurons receive inputs from several V1 subunits with different disparity selectivity. In this paper, we carried out quantitative modelling demonstrating this. I like this paper because much of my work has been on modelling the properties of neurons in V1. It's nice to feel that we can begin to trace how those calculations are then used beyond V1 to result in our depth perception.

Read JCA, Phillipson GP, Glennerster A ( 2009 )
Latitude and longitude vertical disparities

Journal of Vision Vol: 9(13):11 Pages: 1-37 [view on journal website] Pubmed ID : 20055544

All Matlab code required to generate the figures is available here. NB One thing I get with all my old Matlab code is that the abbreviation “fonts” no longer works in recent versions of Matlab; you have to say “fontsize”. So you may need a search and replace on that.
Comment: At around this time I'd been spending a lot of time thinking about vertical disparity, and had been awarded an MRC grant to study it. To begin with, I wasn't even entirely clear what vertical disparity was, and I had difficulty following some of the other papers on it. I realised that a lot of the confusion was occurring because there are actually several different definitions of "vertical disparity" in the literature -- I've identified at least four -- and to make matters worse, different papers aren't always clear about exactly which definition they have in mind. Unsurprisingly, this has caused a lot of confusion about what the properties of vertical disparity actually are. Part of the problem, I think, is that under some circumstances you obtain the same results regardless of whether you define the elevation coordinate as a latitude or a longitude on the retina, and this may have given the impression that it doesn't ever matter -- whereas in fact, under some circumstances, the two definitions give completely different results. So with my PhD student Graeme Phillipson and my old friend and colleague from back in Oxford, Andrew Glennerster, we decided to write a paper really getting into the nitty-gritty of vertical disparity, and laying out clearly what properties follow from different definitions. It may not be the most exciting paper ever, and like many of my papers, it has masses of Appendices filled with equations. But we hoped it would be a useful reference for anyone interested in vertical disparity -- and I did at least try hard to make the pictures pretty.

Read JCA , Cumming BG ( 2007 )
Sensors for impossible stimuli may solve the stereo correspondence problem (Comment on this paper in Nature's Research Highlights section)

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Read JCA , Cumming BG (2007) ( 2007 )
Sensors for impossible stimuli may solve the stereo correspondence problem.

Nature Neuroscience Vol: 10 Pages: 1322 - 1328. [view on journal website] Pubmed ID : 17828262

ERRATA
Supplementary material
Comment on this paper in Nature's Research Highlights section, Nature, 449: 118.
This directory should contain the code I used to generate Fig 3 (instructions on using)
Comment: Here, Bruce and I returned to the question of how to extract stimulus disparity from a population of binocular neurons such as seem to exist in primary visual cortex. Once again, we used the energy model of Ohzawa, DeAngelis and Freeman (1990). The output of this model depends on the receptive fields in the two eyes. The physiological literature shows that the receptive fields are usually well-described by Gabor functions, of similar spatial frequency and orientation tuning, but differing in their phase and/or position on the retina. It makes sense to have receptive fields which differ in retinal position -- you can view these as "position-disparity detectors" sensing objects at different positions in space. But we wondered why you find receptive fields differing in phase, "phase-disparity detectors". These do work as disparity detectors, but they seem suboptimal -- they respond best to retinal patterns that are never generated by real objects. If the brain only contained these phase-disparity detectors, instead of the more suitable position-disparity detectors, you might reckon there was some developmental constraint which meant that the brain just couldn't wire up position-disparity detectors. But since it clearly can generate position-disparity, what's the point of having phase-disparity detectors as well?
Phase-disparity detectors respond best to different patterns of light and dark in the two eyes. Real objects would always project the same pattern in both eyes, so phase-disparity detectors don't respond best to real objects. They respond best to unrelated regions of the visual scene, i.e. where the regions of the two retina viewed by this particular binocular neuron do not correspond to the same object in space. In other words, they respond best to false matches. This could be very useful, because position-disparity detectors are plagued by false matches. It's difficult to interpret their response, as a strong response does not necessarily indicate that there is an object at the disparity to which the detector is tuned; it could be a false match. We realised that you could solve this problem by using the phase-disparity detectors as "lie detectors". For each possible match provided by the position-disparity detectors, the pattern of the response of the corresponding phase-disparity detectors reveals whether the match is true or false.
At the moment, this is just an idea; we don't know if this is really how the brain uses phase-disparity detectors. We hope this paper will stimulate experimental investigations which will either confirm or rule out our suggestion, as well as prompting further consideration about the role of phase disparity in the brain.

Read JCA, Cumming BG ( 2006 )
Does depth perception require vertical disparity detectors?

Journal of Vision Vol: 6(12)1 Pages: 1323-1355 [view on journal website] Pubmed ID : 17209738

Comment: This paper represents a cool idea which turned out (probably) not to be true. There's a wealth of psychophysical evidence indicating that humans measure vertical disparity, and use this to calibrate oculomotor signals about eye position. This has been taken, without much thought, as "obviously" indicating that the brain therefore contains detectors tuned to a range of vertical disparities, and various physiological studies have looked for them (so far with little success, due to a range of interpretation problems). We realised that actually, the psychophysical performance could be explained if the brain only had access to the magnitude (not the sign) of vertical disparity. Essentially, this is because the sign has a predictable pattern, so you don't need to measure it explicitly. This is important because if all you need is the magnitude of vertical disparity, you can get this from a population of purely horizontal disparity detectors. For these detectors, vertical disparity could be deduced via its effect on binocular correlation. This seemed to us a very elegant solution for the brain to adopt. Most disparities are horizontal (see Read & Cumming 2004), so it would enable the brain to concentrate its detectors according to the statistics of natural viewing (clearly the efficient thing to do) while still being able to extract information from vertical disparities when they do occur. This also raised the exciting possibility of being able to mimic vertical-disparity illusions with binocular correlation -- stereopsis without disparity. Sadly, however, my attempts to produce these illusions failed, and I now believe that this idea is not correct. In 2010, I returned to this train of thought and developed a more sophisticated model which can deduce both magnitude and sign of vertical disparity from a population of purely horizontal disparity detectors.

Hardingham NR, Bannister NJ, Read JCA, Fox KD, Hardingham GE, Jack JJB ( 2006 )
Extracellular calcium regulates postsynaptic efficacy through group 1 metabotropic glutamate receptors.

Journal of Neuroscience . Vol: 26(23) Pages: 6337-45 [view on journal website] Pubmed ID : 16763042

Matlab code for quantal analysis
Comment: This project began when I was in my first neuroscience post-doc, doing a Wellcome Training Fellowship in Mathematical Biology with Julian Jack in Oxford. Julian's lab had done a lot of work on synaptic physiology, in particular developing quantal analysis as a tool to examine central synapses. The physiology underlying quantal analysis is the fact that neurons are generally connected by more than one terminal. When the presynaptic neuron fires an action potential, packets - quanta - of neurotransmitter may be released from all, some or none of these terminals. If each packet of neurotransmitter contributes a similar amount to the postsynaptic depolarisation, then a histogram of the effect produced by each presynaptic action potential will have several peaks, corresponding to the release of 0, 1, 2 ... quanta of neurotransmitter. In principle, this histogram can then be analysed to estimate the effect caused by each quantum, and the probability that a quantum will be released from a terminal given an action potential. In practice, this depends critically on things like whether each quantum really does have a very similar postsynaptic effect, whether the release probability is the same at all terminals, whether these quantities are constant over time and so on. Julian's lab had already developed a lot of sophisticated tools for quantal analysis, and I took this further, developing a still more elaborate fitting algorithm to extract the quantal parameters, and also a battery of statistical tests to decide whether the resulting model of the synapse was adequate. There's quite a lot of sceptism as to how far quantal analysis can be trusted in the central nervous system (as opposed to at the neuromuscular junction, where it was originally developed), so these tests were critical in convincing people that our results were reliable. Neil Hardingham, the first author, who was a Ph.D. student and post-doc in Julian's lab when I was there, used these techniques to examine how the quantal parameters change as a function of extracellular calcium. He was able to show that calcium depletion, as well as reducing release probability, also reduces quantal size. Since calcium levels drop as neurons become active, this represents a novel mechanism for regulating information transfer between neurons.

Read JCA, Cumming BG ( 2005 )
All Pulfrich-like illusions can be explained without joint encoding of motion and disparity.

Journal of Vision Vol: 5(11):1 Pages: 901-927 [view on journal website] Pubmed ID : 16441193

ERRATA
The original Matlab .mat data files containing results of the simulations are available here. Code to generate all results figures in the paper from these files is available for download here (MakeFigureX.m files). In the same location, you'll find SimulationForFigureX.m files which should enable you to reproduce the .mat files (subject to the caveat given in the README.docx file).
Comment: The final step was to build a neuronal model, and show that it experienced the illusion. We modelled a neuronal population constructed of neurons which either encoded motion, or depth (not both), and showed that a very simple way of "reading out" this activity, so as to convert it to a perception of depth, would be subject to the Pulfrich illusion. We also examined other evidence which had been put forward in support of the joint motion/depth idea, such as the illusion of swirling motion which occurs in dynamic noise with an interocular delay. We found that this, too, could be experienced by a brain which encoded motion and depth entirely separately. So, while there certainly are primate neurons which jointly encode motion and depth (notably in MT), there is no reason to suppose that these play a privileged role in supporting the Pulfrich effect and related illusions.
This series of three papers (Read & Cumming 2005abc) has recently attracted some criticism from Ning Qian and Ralph Freeman, in a paper entitled "Pulfrich phenomena are coded effectively by a joint motion-disparity process" (J Vis, 9(5): 1-16). My take on it is that we are all basically in agreement, but the situation is obscured by the lack of a clear agreed definition of "joint" vs "separate" encoding of motion and disparity. For example, we said that to be called a motion detector, a cell not only had to be tuned to speed, it also had to respond differently to opposite directions of motion, whereas Qian & Freeman required only speed tuning. I want to clear up one other point. Qian & Freeman say that our model is "non-causal", apparently because it responds to the disparity between a stimulus in one eye and a stimulus which arrives in the other eye at a later time. At the time that stimulus 1 occurs, stimulus 2 is still in the future. However, at the time the neuron responds to the disparity between the two stimuli, both stimuli have already occurred. Thus, the model is firmly causal. Indeed, our derivation of its properties explicitly sets the temporal kernel to zero for future times.

Read JCA, Cumming BG ( 2005 )
The stroboscopic Pulfrich effect is not evidence for the joint encoding of motion and depth.

Journal of Vision Vol: 5(5):3 Pages: 417-434 [view on journal website] Pubmed ID : 16097873

ERRATA Comment: However, this left us with something of a puzzle, as the shifts in disparity tuning which occur with delay (in the cat) had been proposed as a neuronal substrate for the Pulfrich effect. This is a visual illusion which occurs when the image from one eye is delayed: moving objects appear to shift in depth. This had been explained on the basis of cells which are sensitive to both direction of motion and to disparity: i.e. which jointly encode motion and depth. However, in our previous paper we had found that such cells were quite rare in monkey V1 (~10%). It seemed surprising to us that these few cells would cause such an illusion, when the vast majority of cells would not be subject to the illusion on this basis. So, we looked again at whether joint encoding of motion and depth really was necessary for the Pulfrich effect. We found that it wasn't. As previous workers had noted, the Pulfrich effect arises because of cells' finite temporal integration; but finite temporal integration does not necessarily imply direction selectivity. Our results suggested that all cells in V1, even the ones which show no shift in disparity tuning with delay, could potentially support the Pulfrich illusion.

Read JCA, Cumming BG ( 2005 )
The effect of interocular delay on disparity-selective V1 neurons: relationship to stereoacuity and the Pulfrich effect.

Journal of Neurophysiology Vol: 94 Pages: 1541-1553 Pubmed ID : 15788521

Comment: Bruce and I now started looking at the effect of differences in the time, as well as the position, at which corresponding features strike the eyes. Bruce recorded the response of V1 neurons to random-dot patterns with both horizontal spatial disparity, and temporal delay. I analysed this data-set, and found that the shape of the disparity tuning curve was largely independent of the delay; delay simply reduced the amplitude. This was contrary to previous reports in the cat (Anzai et al, 2002, Nature Neuroscience), which had emphasised shifts in disparity tuning as a function of delay. However, linear models (like the energy model) would predict that the disparity tuning only shifts in cells which are direction-selective. We showed that the difference between our results and those from cat could be largely explained by the relative paucity of direction-selective cells in the monkey.

Read JCA ( 2005 )
Early computational processing in binocular vision and depth perception.

Progress in Biophysics and Molecular Biology Vol: 87 Pages: 77-108 [view on journal website] Pubmed ID : 15471592

Comment: In 2005, I was invited to speak at the festschrift in honour of my former PI and mentor, Julian Jack FRS, who had launched my career in neuroscience by agreeing to sponsor me for a Wellcome Training Fellowship in Mathematical Biology. I took the opportunity to get my thoughts into shape on how disparity is represented in early visual cortex and talk about some of our work on the energy model and so on.

Read JCA, Cumming BG ( 2004 )
Understanding the cortical specialization for horizontal disparity.

Neural Computation Vol: 16(10) Pages: 1983-2020 [view on journal website] Pubmed ID : 15333204

ERRATA
Matlab code for the disparity distributions is available here
Comment: In a 2002 Nature paper, Bruce measured the response of disparity-tuned cells in V1 to a full range of two-dimensional disparities. This was unusual, because previous work had either used horizontal disparity (in awake animals), or disparity orthogonal to the preferred orientation of the cell (in anaesthetised animals). Bruce found that the 2D disparity-tuning surfaces of the cells tended to be elongated along the horizontal direction, no matter what the preferred orientation of the cell was. This was a very surprising result, as it completely contradicts the predictions of all existing models. Everyone had always assumed that the tuning to 2D disparity would reflect the cell's orientation tuning. So, my next project was to investigate what sort of model could account for this result.

We came up with two models. The first simply postulated that the cells Bruce recorded from were composed of many subunits, and these were scattered more widely horizontally than vertically. The second involved monocular normalization by appropriately elongated units.

Read JCA, Cumming BG ( 2004 )
Ocular dominance predicts neither strength nor class of disparity selectivity with random-dot stimuli in primate V1.

Journal of Neurophysiology Vol: 91 Pages: 1271-1281 [view on journal website] Pubmed ID : 14523074

ERRATA Comment: We address two unresolved issues concerning the coding of binocular disparity in primary visual cortex. Experimental studies and theoretical models have suggested a relationship between a cell’s ocular dominance,
assessed with monocular stimuli, and its tuning to binocular disparity. First, the disparity energy model of disparity selectivity suggests that there should be a correlation between ocular dominance and the strength of disparity tuning. Second, several studies have reported a relationship between ocular dominance and the shape of the disparity tuning curve, with cells dominated by one eye more likely to have disparity tuning of the tuned-inhibitory type. We investigated both of these relationships in single neurons recorded from the primary visual cortex of awake fixating macaques, using dynamic random-dot patterns as a stimulus. To classify disparity tuning curves quantitatively,
we develop a new measure of symmetry, which can be applied to any function. We find no evidence for any correlation between ocular dominance and the nature of disparity tuning. This places constraints on the circuitry underlying disparity tuning.

Read JCA, Cumming BG ( 2003 )
Measuring V1 receptive fields despite eye movements in awake monkeys.

Journal of Neurophysiology Vol: 90 Pages: 946-960 Pubmed ID : 12711706

Comment: This was a little project we did, looking at a way of getting around uncertainties in measurements of eye position. During vision experiments in the awake monkey, scleral search coils -- hair-thin wires implanted around the animal's eyes -- are used to measure where the animal is looking. This enables you to check that the animals are fixating. However, the animals still make tiny fixational eye movements, which blur receptive field measurements. Some people have also used the coil outputs to correct for these microsaccades, but for this to be valid, the error on the coil outputs would have to be small compared to the scatter in eye position during fixation, and no one had checked that this was really the case. We found that coil measurements were subject to a slow drift. This means that you know where the animal is looking at any given moment only to within 0.1 degree of so, too rough to correct for fixational eye movements. However, because the drift is slow,you have a much more accurate idea of the difference between where the animal is looking now and where he was looking one second ago. We used this fact to do an improved Bayesian estimate of the receptive field profile, removing at least some of the smearing.

Read JCA, Cumming BG ( 2003 )
Testing quantitative models of binocular disparity selectivity in primary visual cortex.

Journal of Neurophysiology Vol: 90 Pages: 2795-2817

Comment: This paper represents the first major project I did after coming to work with Bruce. Here, we set out to test some more predictions of the energy model, and compare them with the predictions of the model proposed in Read et al. (2002). One prediction of the energy model is that the Fourier power spectrum of the disparity tuning curve is simply the product of the spatial frequency tuning measured in each of the two eyes. We showed that this isn't true in real cells. Real disparity tuning curves do not tend to have as strong oscillations as you would expect from the band-pass spatial frequency tuning in V1. You might think this could be explained by a relatively trivial modification of the energy-model -- suppose real cells receive input from several subunits with some jitter in their preferred disparity. This could smear out side-lobes which would otherwise have been observed. However, we were able to show that this simple generalisation of the energy-model could not explain the data either. It seems you need a more serious modification.

We showed that the model we'd proposed previously, Read et al. 2002, does seem to be able to account for the data. The key feature which makes this possible is that it allows non-linearities before binocular combination, whereas the energy model is linear up to binocular combination. (Unfortunately, it's this very linearity which makes the energy model so easy to handle mathematically!) We also pointed out that a non-linearity before binocular combination seems necessary in order to explain the behaviour of cells in which one eye always has a suppressive effect.

Read JCA ( 2002 )
A Bayesian model of stereo depth / motion direction discrimination.

Biological Cybernetics Vol: 82 Pages: 117-136 [view on journal website] Pubmed ID : 11911114

ERRATA Comment: While working with Richard, I had begun trying to build a quantitative model of the stereo and motion systems which could explain our psychophysical results. After his death, I continued this work, and eventually wrote it up as the paper above. Again, I'm very grateful to Bruce, Simon and Andrew Glennerster for reading drafts of this and giving me feedback.

An interesting property of anti-correlated stimuli is that, under almost all reasonable assumptions about how disparity might be encoded, different spatial-frequency/orientation channels return different estimates of stimulus disparity. The problem in the model was finding a good way to combine the answers from different channels. In the end, I decided that the best way was to convert each channel's output into a common language, namely a Bayesian probability estimate of disparity. Suppose you have a binocular neuron tuned to disparity D, and you know that the input from the left eye is L. Then you can calculate the expected response of the neuron under the assumption that the stimulus disparity is D, because then the input from the right eye should be the same as that from the left, apart from small differences due to noise. If the actual response of the neuron is very different from this, then it isn't very likely that D really is the disparity of the stimulus.

I was expecting to have to build different ways of combining the different channels' outputs for the two systems, motion and stereo, in order to explain the differences in perception. But, to my surprise, I found that I could use the same mathematical structure. Differences in performance could be captured quite well by just assuming that the motion system is subject to a greater noise level than the stereo system, and that the stereo system prefers small disparities more than the motion system prefers lower speeds.

Read JCA ( 2002 )
A Bayesian approach to the stereo correspondence problem.

Neural Computation Vol: 14 Pages: 1371-1392 Pubmed ID : 12020451

Comment: I got quite interested in the idea of converting the outputs of different channels to probability. I wondered whether the visual system might possibly represent the correspondence problem in probabilistic terms. We tend to pose the correspondence problem in terms of finding "the" matching feature in the right eye for a given feature in the left eye. However, sometimes there may be two matches for a given feature (Panum's limiting case), and sometimes none (occlusion). So, it might make sense to use a concept like probability -- where it is quite possible for two disparities to be considered likely, or none -- rather than a winner-take-all model which enforces exactly one match. I applied the model developed in the previous paper to various test stimuli, and it generally behaved sensibly. Because it was constructed from V1 neurons with a constant disparity preference across their receptive fields, it had a built-in preference for smoothly-varying disparity fields, so it gave correct percepts for the double-nail stimulus. It produced two probability peaks for Panum's limiting case, but only one for a random-dot stereogram. The question of when the visual system produces two disparity values, as in transparency, and how it handles occlusion, is a very interesting one, and this paper certainly goes nowhere near far enough in explaining this.

Read JCA, Parker AJ, Cumming BG ( 2002 )
A simple model accounts for the response of disparity-tuned V1 neurons to anti-correlated images.

Visual Neuroscience Vol: 19 Pages: 735-753 Pubmed ID : 12688669

ERRATA
Matlab Code
Comment: I did my second M. Sc. project under the supervision of Bruce Cumming and Andrew Parker in the Physiology Laboratory at Oxford, and this turned out to be the beginning of a long and fruitful collaboration which saw me moving to the States for 4 years. My project related to an interesting observation Andrew and Bruce had just made in their influentual Nature paper of 1997. This tied in nicely with my project with Richard, because it also involved anti-correlated stimuli. Bruce and Andrew had measured the response of disparity-sensitive neurons in V1 to anti-correlated random-dot stereograms. The highly successful energy model of these neurons, proposed 7 years earlier by Ohzawa, DeAngelis and Freeman in Science, predicted that their disparity tuning curves should invert when they were probed with anti-correlated stimuli. Sure enough, in a triumph for theoretical neuroscience, the curves did invert. However, their amplitude also decreased, and this was not predicted by the model. Because anti-correlated stimuli do not cause a perception of depth, it was possible that this reduction in amplitude represented feedback (or the absence of expected feedback) from higher brain areas. However, it was also possible that a suitable feedforward model might also give a reduced amplitude for anti-correlated stimuli. Andrew and Bruce asked me to see if I could find such a model.
It turned out to be quite simple to modify the stereo energy model to produce this. All you have to do is apply half-wave rectification before inputs from the two eyes are combined, as opposed to after binocular combination as in the energy model. So, the reduction in amplitude does not necessarily depend on feedback from extrastriate areas.
In theory, I would have used this modified version of the energy model in all my subsequent modelling, on the grounds that it more accurately captures the behaviour of real neurons. However, the energy model is very easy to analyse mathematically, whereas the additional non-linearity makes my model almost impossible to say anything about analytically (at least, I haven't been able to!). So, in most of my subsequent population models, I have used the energy model to describe V1 cells. I feel quite fond of this paper, because it was my first encounter with the wonderful stereo energy model of Ohzawa et al. 1990. Much of my subsequent work has been trying to understand the behaviour of this deceptively simple model.

Stephan KE, Heimel J-A F, Read JCA ( 2000 )
The European Union Advanced Course in Computational Neuroscience: linking theoretical and experimental neurosciences.

Boehringer Ingelheim Fonds Futura Vol: 15(1) Pages: 5-14

Read JCA, Eagle RA ( 2000 )
Reversed stereo depth and motion direction with anti-correlated stimuli

Vision Research Vol: 40 Pages: 3345-3358 [view on journal website] Pubmed ID : 11058733

ERRATA Comment: This was my first paper in the field of neuroscience. It represents work I did as an M.Sc. project with Richard Eagle, in the psychology department of Oxford University. Richard died very suddenly, aged 32, while we were working on this project, a personal tragedy for his friends and family and a great loss to vision science. I am very grateful to Simon Prince and Bruce Cumming for their kindness in helping me to write this up, and to Randy Blake, who as editor of Vision Research understood that it was difficult for me to submit my first paper in the field after Richard had died, and wrote me an encouraging letter to accompany the referees' reports.

A stereogram and a two-frame kinematogram presents analogous correspondence problems, in that both require matching features in one image with partners in a second. So one might expect there to be similarities in the way the visual system solves the correspondence problem in each case. On the other hand, there are also obvious differences which one would expect the visual system to exploit: most notably, although we used only horizontal motion in our experiments, motion can in principle occur in any direcion, whereas stereoscopic disparities are overwhelmingly horizontal (a point I later investigated in Read & Cumming 2004b). Richard was interested in examining further a result in the literature which suggested quite a fundamental difference between the two systems. This concerned anti-correlated stimuli, in which one image is replaced with its photographic negative. Anti-correlated random-dot kinematograms produce a reversed perception of depth, whereas anti-correlated random-dot stereograms produce no depth percept at all. Yet, for sinusoidal gratings, both systems must produce a reversed percept, since an anti-correlated sine-grating stereogram with near disparity is exactly the same stimulus as a correlated stereogram with far disparity. So for sufficiently narrow-band stimuli, the two systems must produce the same result, whereas at broader bandwidths, the literature showed they produced different results. With Richard, I examined human perception for filtered 1/f noise at a range of spatial frequency and orientation bandwidths. We found that for one-dimensional stimuli, containing only vertical orientations, both motion and stereo produced rather similar results, with anti-correlated stereograms causing weak reversed depth. However, for two-dimensional stimuli, containing all orientations, anti-correlated stereograms caused no depth percept, in agreement with previous studies, whereas anti-correlated kinematograms caused reversed motion. We suggested that this might be related to the anisotropy in stereo -- that disparities are overwhelmingly horizontal -- and that therefore conflict between different channels had a more devastating impact on depth perception.

Evans NW, Read JCA ( 1998 )
Stability of power-law discs II. The global spiral modes.

Monthly Notices of the Royal Astronomical Society Vol: 300 Pages: 106-130 [view on journal website]

Comment: This paper contains the results of our analysis.

Evans NW, Read JCA ( 1998 )
Stability of power-law discs I. The Fredholm integral equation

Monthly Notices of the Royal Astronomical Society Vol: 300 Pages: 83-105 [view on journal website]

Comment: It seems a lifetime away now, but I began my scientific career in astrophysics, with a doctorate on galactic dynamics supervised by Wyn Evans. For my thesis work, we modelled a disk galaxy as an infinitesimally thin disk, whose density (mass per unit area) varied as an inverse power law of radius. We calculated the stability of this disk to gravitational perturbations within the plane of the disk. The stars in the disk have a tendency to clump together because of their mutual gravitational attraction, so you might think the disk would just collapse into its centre. However, if the disk is spinning fast enough, the tangential motion of the stars will counteract this tendency, and the disk may remain stable. We examined the circumstances under which stable modes are possible, for a variety of different assumptions about the density profile of the disk. This paper is basically the mathematical methods we used to do the analysis.

Read JCA ( 1997 )
The stability of model disk galaxies

D. Phil. thesis, University of Oxford. Vol: Pages:

Jones L ( )
JonesPhDThesis2017

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Comment: Lisa's PhD thesis

Yazdani P ( )
Yazdani2016PhD

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Comment: The spread of epileptic activity within the cortex is opposed by a powerful inhibitory restraint. We hypothesized that the same inhibitory mechanisms are likely also to underlie the phenomenon of centre-surround suppression. In this thesis, I used different non-invasive visual psychophysical assays of surround suppression to answer whether they can be used as a measurement of network state in epilepsy and as a way of predicting seizures.
We recruited 146 healthy volunteer controls and 54 patients with clinically confirmed epilepsy. Three different stimulus paradigms (motion direction discrimination, contrast detection and orientation discrimination tasks) were used to derive surround suppression indices which are believed to reflect the strength of cortical inhibition.
Our results suggest that motion and contrast surround suppression phenomena are not related. We found that suppression indices for the different tests in individual participants were not significantly correlated. In addition, multivariate regression analyses showed that motion suppression index was predicted strongly by age and seizure type, but not by seizure frequency. Specifically, we found that patients with exclusively focal epilepsy, and no history of generalization, showed significantly stronger cortical inhibition as measured by the surround suppression index compared to all other groups, including controls. In contrast, patients with focal seizures evolving into generalised seizures, and patients with generalised genetic epilepsy, showed a similar level of cortical inhibition to controls.
To answer whether psychophysical tests can be used as a way of predicting seizures, a longitudinal study was designed, deriving repeated measures of suppression indices in individuals. The results indicated no strong link between timing of seizures and suppression indices in patients.
In conclusion, visual psychophysics provides a simple and non-invasive means of assessing the state of inhibitory networks involved in the pathophysiology of epilepsy. The inability to increase activity in inhibitory networks in response to focal epileptic seizure may predict the risk of generalised seizures, which may in turn allow stratification of SUDEP risk.

Allenmark FP ( )
Allenmark2011PhD

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Comment: Fredrik Allenmark's PhD thesis

Read JCA , Cumming BG ( )
Sensors for impossible stimuli may solve the stereo correspondence problem (Supplementary material)

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Comment: Here, we returned to the question of how to extract stimulus disparity from a population of binocular neurons such as seem to exist in primary visual cortex. Once again, we used the energy model of Ohzawa, DeAngelis and Freeman (199). The output of this model depends on the receptive fields in the two eyes. The physiological literature shows that the receptive fields are usually well-described by Gabor functions, of similar spatial frequency and orientation tuning, but differing in their phase and/or position on the retina. It makes sense to have receptive fields which differ in retinal position -- you can view these as "position-disparity detectors" sensing objects at different positions in space. But we wondered why you find receptive fields differing in phase, "phase-disparity detectors". These do work as disparity detectors, but they seem suboptimal -- they respond best to retinal patterns that are never generated by real objects. If the brain only contained these phase-disparity detectors, instead of the more suitable position-disparity detectors, you might reckon there was some developmental constraint which meant that the brain just couldn't wire up position-disparity detectors. But since it clearly can generate position-disparity, what's the point of having phase-disparity detectors as well?

Phase-disparity detectors respond best to different patterns of light and dark in the two eyes. Real objects would always project the same pattern in both eyes, so phase-disparity detectors don't respond best to real objects. They respond best to unrelated regions of the visual scene, i.e. where the regions of the two retina viewed by this particular binocular neuron do not correspond to the same object in space. In other words, they respond best to false matches. This could be very useful, because position-disparity detectors are plagued by false matches. It's difficult to interpret their response, as a strong response does not necessarily indicate that there is an object at the disparity to which the detector is tuned; it could be a false match. We realised that you could solve this problem by using the phase-disparity detectors as "lie detectors". For each possible match provided by the position-disparity detectors, the pattern of the response of the corresponding phase-disparity detectors reveals whether the match is true or false.

At the moment, this is just an idea; we don't know if this is really how the brain uses phase-disparity detectors. We hope this paper will stimulate experimental investigations which will either confirm or rule out our suggestion, as well as prompting further consideration about the role of phase disparity in the brain.

Read JCA ( )
Efficient estimation of stereo thresholds: What slope should be assumed for the psychometric function?

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Read JCA ( )
Quantal-analysis2

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