Search tips
Search criteria

Results 1-25 (1140849)

Clipboard (0)

Related Articles

1.  Learning to identify contrast-defined letters in peripheral vision 
Vision research  2005;46(6-7):1038-1047.
Performance for identifying luminance-defined letters in peripheral vision improves with training. The purpose of the present study was to examine whether performance for identifying contrast-defined letters also improves with training in peripheral vision, and whether any improvement transfers to luminance-defined letters. Eight observers were trained to identify contrast-defined letters presented singly at 10° eccentricity in the inferior visual field. Before and after training, we measured observers’ thresholds for identifying luminance-defined and contrast-defined letters, embedded within a field of white luminance noise (maximum luminance contrast = 0, 0.25, and 0.5), at the same eccentric location. Each training session consisted of 10 blocks (100 trials per block) of identifying contrast-defined letters at a background noise contrast of 0.5. Letters (x-height = 4.2°) were the 26 lowercase letters of the Times-Roman alphabet. Luminance-defined letters were generated by introducing a luminance difference between the stimulus letter and its mid-gray background. The background noise covered both the letter and its background. Contrast-defined letters were generated by introducing a differential noise contrast between the group of pixels that made up the stimulus letter and the group of pixels that made up the background. Following training, observers showed a significant reduction in threshold for identifying contrast-defined letters (p < 0.0001). Averaged across observers and background noise contrasts, the reduction was 25.8%, with the greatest reduction (32%) occurring at the trained background noise contrast. There was virtually no transfer of improvement to luminance-defined letters, or to an untrained letter size (2× original), or an untrained retinal location (10° superior field). In contrast, learning transferred completely to the untrained contralateral eye. Our results show that training improves performance for identifying contrast-defined letters in peripheral vision. This perceptual learning effect seems to be stimulus-specific, as it shows no transfer to the identification of luminance-defined letters. The complete interocular transfer, and the retinotopic (retinal location) and size specificity of the learning effect are consistent with the properties of neurons in early visual area V2.
PMCID: PMC2747643  PMID: 16337252
Letter recognition; Peripheral vision; Perceptual learning; Second-order
2.  Effect of luminance noise on the object frequencies mediating letter identification 
Purpose: To determine if the same object frequency information mediates letter contrast threshold in the presence and absence of additive luminance noise (i.e., “noise-invariant processing”) for letters of different size.
Methods: Contrast thresholds for Sloan letters ranging in size from 0.9 to 1.8 log MAR were obtained from three visually normal observers under three paradigms: (1) high- and low-pass Gaussian filtered letters were presented against a uniform adapting field; (2) high- and low-pass Gaussian filtered letters were presented in additive white luminance noise; and (3) unfiltered letters were presented in high- and low-pass Gaussian filtered luminance noise. A range of high- and low-pass filter cutoffs were used to limit selectively the object frequency content of the letters (paradigms 1 and 2) or noise (paradigm 3). The object frequencies mediating letter identification under each paradigm were derived from plots of log contrast threshold vs. log filter cutoff frequency.
Results: The object frequency band mediating letter identification systematically shifted to higher frequencies with increasing log MAR letter size under all three paradigms. However, the relationship between object frequency and letter size depended on the paradigm under which the measurements were obtained. The largest difference in object frequency among the paradigms was observed at 1.8 log MAR, where the addition of white noise nearly doubled the center frequency of the band of object frequencies mediating letter identification, compared to measurements made in the absence of noise.
Conclusion: Noise can affect the object frequency band mediating letter contrast threshold, particularly for large letters, an effect that is likely due to strong masking of the low frequency letter components by low frequency noise checks. This finding indicates that noise-invariant processing cannot necessarily be assumed for large letters presented in white noise.
PMCID: PMC4080385  PMID: 25071637
visual noise; letter identification; contrast sensitivity; optotype; object spatial frequency; retinal spatial frequency
3.  Intrasaccadic suppression is dominated by reduced detector gain 
Journal of Vision  2013;13(8):4.
Human vision requires fast eye movements (saccades). Each saccade causes a self-induced motion signal, but we are not aware of this potentially jarring visual input. Among the theorized causes of this phenomenon is a decrease in visual sensitivity before (presaccadic suppression) and during (intrasaccadic suppression) saccades. We investigated intrasaccadic suppression using a perceptual template model (PTM) relating visual detection to different signal-processing stages. One stage changes the gain on the detector's input; another increases uncertainty about the stimulus, allowing more noise into the detector; and other stages inject noise into the detector in a stimulus-dependent or -independent manner. By quantifying intrasaccadic suppression of flashed horizontal gratings at varying external noise levels, we obtained threshold-versus-noise (TVN) data, allowing us to fit the PTM. We tested if any of the PTM parameters changed significantly between the fixation and saccade models and could therefore account for intrasaccadic suppression. We found that the dominant contribution to intrasaccadic suppression was a reduction in the gain of the visual detector. We discuss how our study differs from previous ones that have pointed to uncertainty as an underlying cause of intrasaccadic suppression and how the equivalent noise approach provides a framework for comparing the disparate neural correlates of saccadic suppression.
PMCID: PMC3704127  PMID: 23820025
saccadic suppression; perceptual template model; equivalent noise; eye movements; noise injection; gain reduction; spatial uncertainty
4.  Learning to Identify Near-Threshold Luminance-Defined and Contrast-Defined Letters in Observers with Amblyopia 
Vision research  2008;48(27):2739-2750.
We assessed whether or not the sensitivity for identifying luminance-defined and contrast-defined letters improved with training in a group of amblyopic observers who have passed the critical period of development. In Experiment 1, we tracked the contrast threshold for identifying luminance-defined letters with training in a group of 11 amblyopic observers. Following training, six observers showed a reduction in thresholds, averaging 20%, for identifying luminance-defined letters. This improvement transferred extremely well to the untrained task of identifying contrast-defined letters (average improvement = 38%) but did not transfer to an acuity measurement. Seven of the 11 observers were subsequently trained on identifying contrast-defined letters in Experiment 2. Following training, five of these seven observers demonstrated a further improvement, averaging 17%, for identifying contrast-defined letters. This improvement did not transfer to the untrained task of identifying luminance-defined letters. Our findings are consistent with predictions based on the locus of learning for first- and second-order stimuli according to the filter-rectifier-filter model for second-order visual processing.
PMCID: PMC2642955  PMID: 18824189
Amblyopia; Perceptual learning; Training; First-order; Second-order; Letter recognition
5.  Modeling mechanisms of perceptual learning with augmented Hebbian re-weighting 
Vision research  2009;50(4):375-390.
Using the external noise plus training paradigm, we have consistently found that two independent mechanisms, stimulus enhancement and external noise exclusion, support perceptual learning in a range of tasks. Here, we show that re-weighting of stable early sensory representations through Hebbian learning (Petrov et al., 2005, 2006) can generate performance patterns that parallel a large range of empirical data: (1) perceptual learning reduced contrast thresholds at all levels of external noise in peripheral orientation identification (Dosher & Lu, 1998, 1999), (2) training with low noise exemplars transferred to performance in high noise, while training with exemplars embedded in high external noise transferred little to performance in low noise (Dosher & Lu, 2005), and (3) pre-training in high external noise only reduced subsequent learning in high external noise, whereas pre-training in zero external noise left very little additional learning in all the external noise conditions (Lu et al., 2006). In the augmented Hebbian re-weighting model (AHRM), perceptual learning strengthens or maintains the connections between the most closely tuned visual channels and a learned categorization structure, while it prunes or reduces inputs from task-irrelevant channels. Reducing the weights on irrelevant channels reduces the contributions of external noise and additive internal noise. Manifestation of stimulus enhancement or external noise exclusion depends on the initial state of internal noise and connection weights in the beginning of a learning task. Both mechanisms reflect re-weighting of stable early sensory representations.
PMCID: PMC2824067  PMID: 19732786
Re-weighting; Hebbian learning; Stimulus enhancement; External noise exclusion; Mechanisms of perceptual learning
6.  Identification of contrast-defined letters benefits from perceptual learning in adults with amblyopia 
Vision research  2006;46(22):3853-3861.
Amblyopes show specific deficits in processing second-order spatial information (e.g. Wong, Levi, & McGraw (2001). Is second-order spatial loss in amblyopia explained by the loss of first-order spatial input? Vision Research, 41, 2951–2960). Recent work suggests there is a significant degree of plasticity in the visual pathway that processes first-order spatial information in adults with amblyopia. In this study, we asked whether or not there is similar plasticity in the ability to process second-order spatial information in adults with amblyopia. Ten adult observers with amblyopia (five strabismic, four anisometropic and one mixed) were trained to identify contrast-defined (second-order) letters using their amblyopic eyes. Before and after training, we determined observers’ contrast thresholds for identifying luminance-defined (first-order) and contrast-defined letters, separately for the non-amblyopic and amblyopic eyes. Following training, eight of the 10 observers showed a significant reduction in contrast thresholds for identifying contrast-defined letters with the amblyopic eye. Five of these observers also showed a partial transfer of improvement to their fellow untrained non-amblyopic eye for identifying contrast-defined letters. There was a small but statistically significant transfer to the untrained task of identifying luminance-defined letters in the same trained eye. Similar to first-order spatial tasks, adults with amblyopia benefit from perceptual learning for identifying contrast-defined letters in their amblyopic eyes, suggesting a sizeable degree of plasticity in the visual pathway for processing second-order spatial information.
PMCID: PMC1852540  PMID: 16930666
Amblyopia; Letter recognition; Perceptual learning; Second-order
7.  Aging, Perceptual learning, and Changes in Efficiency of Motion Processing 
Vision Research  2011;61:144-156.
In the present study we examined the use of perceptual learning to improve motion processing in older and younger individuals. Using the Perceptual Template Model (Lu & Dosher, 1998; 1999), age-related differences in baseline perceptual inefficiencies and changes due to training were assessed for additive internal noise, tolerance to external noise, and internal multiplicative noise. In Experiments 1 and 2 we trained participants by manipulating contrast in noise embedded sine-wave gratings and Random Dot Cinematograms (RDCs). The results indicate that older observers have higher additive internal noise and lower tolerance to external noise compared to younger observers. The rate of perceptual learning in older observers was found to be similar to that of younger observers suggesting that plasticity of motion processing mechanisms is well preserved in advancing age. Transfer of learning between sine-wave gratings and RDCs for both older and younger observers was examined in an analysis of pre/post-test measurements. The results indicate that transfer of learning occurred for both age groups. This suggests that older individuals maintain a sufficient degree of plasticity to allow generalization between sine-wave gratings and RDCs. In addition, training with RDCs was found to produce greater perceptual learning than training with sine-wave gratings. These experiments provide important findings regarding changes in perceptual efficiency for motion perception in older adults and suggest that perceptual learning is an effective approach for recovering from age-related declines in visual processing.
PMCID: PMC3226881  PMID: 21807016
aging; perceptual learning; motion; modeling; perceptual efficiency
8.  Noise Provides New Insights on Contrast Sensitivity Function 
PLoS ONE  2014;9(3):e90579.
Sensitivity to luminance difference, or contrast sensitivity, is critical for animals to survive in and interact with the external world. The contrast sensitivity function (CSF), which measures visual sensitivity to spatial patterns over a wide range of spatial frequencies, provides a comprehensive characterization of the visual system. Despite its popularity and significance in both basic research and clinical practice, it hasn’t been clear what determines the CSF and how the factors underlying the CSF change in different conditions. In the current study, we applied the external noise method and perceptual template model to a wide range of external noise and spatial frequency (SF) conditions, and evaluated how the various sources of observer inefficiency changed with SF and determined the limiting factors underlying the CSF. We found that only internal additive noise and template gain changed significantly with SF, while the transducer non-linearity and coefficient for multiplicative noise were constant. The 12-parameter model provided a very good account of all the data in the 200 tested conditions (86.5%, 86.2%, 89.5%, and 96.4% for the four subjects, respectively). Our results suggest a re-consideration of the popular spatial vision model that employs the CSF as the front-end filter and constant internal additive noise across spatial frequencies. The study will also be of interest to scientists and clinicians engaged in characterizing spatial vision deficits and/or developing rehabilitation methods to restore spatial vision in clinical populations.
PMCID: PMC3953123  PMID: 24626135
9.  Size or spacing: Which limits letter recognition in people with age-related macular degeneration? 
Vision research  2014;101:167-176.
Recent evidence suggests a double dissociation of size and spacing limit on letter recognition — it is limited by size in the fovea and critical spacing in the normal periphery. Here, we evaluated whether size or spacing limits letter recognition in people with age-related macular degeneration (AMD) who must use their peripheral vision. We measured the size threshold for recognizing lowercase letters presented alone, or flanked by two letters at various center-to-center nominal letter spacings (multiples of letter size) for 11 observers with AMD. For comparison, similar measurements were obtained at 5 and 10° eccentricity in the nasal and lower visual fields in three older adults with normal vision. Single-letter size thresholds were worse for observers with AMD than at comparable retinal locations in the normal periphery. For flanked letters, size threshold improved with larger nominal spacing up to the critical spacing, beyond which size threshold was unaffected by the flankers. Seven AMD observers had a nominal critical spacing between 1.25× and 1.80×, values close to those in the normal fovea, suggesting that their letter recognition is size-limited; two had a nominal critical spacing of 3–4×, values close to those in the normal periphery, implying that their letter recognition is limited by spacing; and another two had a nominal critical spacing of ~2.3×, implying that their letter recognition is limited by both size and spacing. The wide range of nominal critical spacings observed in our AMD observers may reflect the degree of completeness of their adaptation process to vision loss.
PMCID: PMC4169903  PMID: 25014400
letter recognition; crowding; age-related macular degeneration; peripheral vision
10.  Efficient integration across spatial frequencies for letter identification in foveal and peripheral vision 
Journal of vision  2008;8(13):3.1-320.
Objects in natural scenes are spatially broadband; in contrast, feature detectors in the early stages of visual processing are narrowly tuned in spatial frequency. Earlier studies of feature integration using gratings suggested that integration across spatial frequencies is suboptimal. Here we re-examined this conclusion using a letter identification task at the fovea and at 10 deg in the lower visual field. We found that integration across narrow-band (1-octave) spatial frequency components of letter stimuli is optimal in the fovea. Surprisingly, this optimality is preserved in the periphery, even though feature integration is known to be deficient in the periphery from studies of other form-vision tasks such as crowding. A model that is otherwise a white-noise ideal observer except for a limited spatial resolution defined by the human contrast sensitivity function and using internal templates slightly wider in bandwidth than the stimuli is able to account for the human data. Our findings suggest that deficiency in feature integration found in peripheral vision is not across spatial frequencies.
PMCID: PMC2635099  PMID: 19146333
spatial frequency channels; summation; letter identification; fovea; periphery
11.  Developmental mechanisms underlying improved contrast thresholds for discriminations of orientation signals embedded in noise 
We combined an external noise paradigm with an efficient procedure for obtaining contrast thresholds (Lesmes et al., 2006) in order to model developmental changes in the effect of noise on contrast discrimination during childhood. Specifically, we measured the contrast thresholds of 5-, 7-, 9-year-olds and adults (n = 20/age) in a two alternative forced-choice orientation discrimination task over a wide range of external noise levels and at three levels of accuracy. Overall, as age increased, contrast thresholds decreased over the entire range of external noise levels tested. The decrease was greatest between 5 and 7 years of age. The reduction in threshold after age 5 was greater in the high than the low external noise region, a pattern implying greater tolerance of the irrelevant background noise as children became older. To model the mechanisms underlying these developmental changes in terms of internal noise components, we adapted the original perceptual template model (Lu and Dosher, 1998) and normalized the magnitude of performance changes against the performance of 5-year-olds. The resulting model provided an excellent fit (r2 = 0.985) to the contrast thresholds at multiple levels of accuracy (60, 75, and 90%) across a wide range of external noise levels. The improvements in contrast thresholds with age were best modeled by a combination of reductions in internal additive noise, reductions in internal multiplicative noise, and improvements in excluding external noise by template retuning. In line with the data, the improvement was greatest between 5 and 7 years of age, accompanied by a 39% reduction in additive noise, 71% reduction in multiplicative noise, and 45% improvement in external noise exclusion. The modeled improvements likely reflect developmental changes at the cortical level, rather than changes in front-end structural properties (Kiorpes et al., 2003).
PMCID: PMC4157613  PMID: 25249993
vision; contrast thresholds; internal noise; development; psychophysics
12.  Characterizing Perceptual Performance at Multiple Discrimination Precisions in External Noise 
Existing observer models developed for studies with the external noise paradigm are strictly only applicable to target detection or identification/discrimination of orthogonal target(s). We elaborated the perceptual template model (PTM) to account for contrast thresholds in identifying non-orthogonal targets. Full contrast psychometric functions were measured in an orientation identification task with four orientation differences across a wide range of external noise levels. We showed that observer performance can be modeled by the elaborated PTM with two templates that correspond to the two stimulus categories. Sampling efficiencies of the human observers were also estimated. The elaborated PTM provides a theoretical framework to characterize joint feature and contrast sensitivity of human observers.
PMCID: PMC2829446  PMID: 19884915
13.  Complete Transfer of Perceptual Learning across Retinal Locations Enabled by Double Training 
Current biology : CB  2008;18(24):1922-1926.
Practice improves discrimination of many basic visual features, such as contrast, orientation, positional offset, etc. [1–7]. Perceptual learning of many of these tasks is found to be retinal location specific, in that learning transfers little to an untrained retinal location [1, 6–8]. In most perceptual learning models, this location specificity is interpreted as a pointer to a retinotopic early visual cortical locus of learning [1, 6–11]. Alternatively, an untested hypothesis is that learning could occur in a central site, but it consists of two separate aspects: learning to discriminate a specific stimulus feature (“feature learning”), and learning to deal with stimulus non-specific factors like local noise at the stimulus location (“location learning”) [12]. Therefore, learning is not transferable to a new location that has never been location-trained. To test this hypothesis we developed a novel double-training paradigm that employed conventional feature training (e.g., contrast) at one location, and additional training with an irrelevant feature/task (e.g. orientation) at a second location, either simultaneously or at a different time. Our results showed that this additional location training enabled a complete transfer of feature learning (e.g., contrast) to the second location. This finding challenges location specificity and its inferred cortical retinotopy as central concepts to many perceptual learning models, and suggests perceptual learning involves higher non-retinotopic brain areas that enable location transfer.
PMCID: PMC3045109  PMID: 19062277
14.  Learning to identify crowded letters: Does the learning depend on the frequency of training? 
Vision research  2012;77:41-50.
Performance for many visual tasks improves with training. The magnitude of improvement following training depends on the training task, number of trials per training session and the total amount of training. Does the magnitude of improvement also depend on the frequency of training sessions? In this study, we compared the learning effect for three groups of normally sighted observers who repeatedly practiced the task of identifying crowded letters in the periphery for six sessions (1000 trials per session), according to three different training schedules — one group received one session of training everyday, the second group received a training session once a week and the third group once every two weeks. Following six sessions of training, all observers improved in their performance of identifying crowded letters in the periphery. Most importantly, the magnitudes of improvement were similar across the three training groups. The improvement was accompanied by a reduction in the spatial extent of crowding, an increase in the size of visual span and a reduction in letter-size threshold. The magnitudes of these accompanied improvements were also similar across the three training groups. Our finding that the effectiveness of visual perceptual learning is similar for daily, weekly and biweekly training has significant implication for adopting perceptual learning as an option to improve visual functions for clinical patients.
PMCID: PMC3538889  PMID: 23206551
perceptual learning; crowding; letter identification; peripheral vision
15.  Ideal observer analysis of crowding and the reduction of crowding through learning 
Journal of vision  2010;10(5):16.
Crowding is a prominent phenomenon in peripheral vision where nearby objects impede one’s ability to identify a target of interest. The precise mechanism of crowding is not known. We used ideal observer analysis and a noise-masking paradigm to identify the functional mechanism of crowding. We tested letter identification in the periphery with and without flanking letters and found that crowding increases equivalent input noise and decreases sampling efficiency. Crowding effectively causes the signal from the target to be noisier and at the same time reduces the visual system’s ability to make use of a noisy signal. After practicing identification of flanked letters without noise in the periphery for 6 days, subjects’ performance for identifying flanked letters improved (reduction of crowding). Across subjects, the improvement was attributable to either a decrease in crowding-induced equivalent input noise or an increase in sampling efficiency, but seldom both. This pattern of results is consistent with a simple model whereby learning reduces crowding by adjusting the spatial extent of a perceptual window used to gather relevant input features. Following learning, subjects with inappropriately large windows reduced their window sizes; while subjects with inappropriately small windows increased their window sizes. The improvement in equivalent input noise and sampling efficiency persists for at least 6 months.
PMCID: PMC3096759  PMID: 20616136
peripheral vision; crowding; perceptual learning; ideal observer analysis
16.  Spatial Contrast Sensitivity in Dynamic and Static Additive Luminance Noise 
Vision research  2010;50(19):1957-1965.
The purpose of this study was to define the quantitative relationship between the temporal characteristics of additive luminance noise and the properties of the spatial contrast sensitivity function (CSF). CSFs were obtained from two observers using Gabor patch targets of short duration that were added to white luminance noise with a range of root-mean-square contrasts (crms). The noise was either dynamic or static and was either of the same duration as the test target (synchronous) or of longer duration (asynchronous). For targets presented in asynchronous dynamic, synchronous dynamic, and synchronous static noise, the CSFs became increasingly band-pass with increasing crms, whereas the CSFs were low-pass at all levels of crms for targets presented in asynchronous static noise. For all noise types, the properties of the CSFs were well-predicted by the linear amplifier model (LAM), in which the signal energy at threshold (Et) is related linearly to noise spectral density (N). The fundamentally different characteristics of CSFs obtained in asynchronous static noise can be accounted for by a previous proposal that this noise type biases contrast sensitivity toward transient (inferred magnocellular) mechanisms. The other three modes of noise presentation appear to emphasize detection by sustained (inferred parvocellular) mechanisms.
PMCID: PMC2926298  PMID: 20638404
contrast sensitivity; spatial vision; visual noise; sustained/transient; magnocellular/parvocellular
17.  Broad-based visual benefits from training with an integrated perceptual-learning video game 
Vision research  2014;99:134-140.
Perception is the window through which we understand all information about our environment, and therefore deficits in perception due to disease, injury, stroke or aging can have significant negative impacts on individuals’ lives. Research in the field of perceptual learning has demonstrated that vision can be improved in both normally seeing and visually impaired individuals, however, a limitation of most perceptual learning approaches is their emphasis on isolating particular mechanisms. In the current study, we adopted an integrative approach where the goal is not to achieve highly specific learning but instead to achieve general improvements to vision. We combined multiple perceptual learning approaches that have individually contributed to increasing the speed, magnitude and generality of learning into a perceptual-learning based video-game. Our results demonstrate broad-based benefits of vision in a healthy adult population. Transfer from the game includes; improvements in acuity (measured with self-paced standard eye-charts), improvement along the full contrast sensitivity function, and improvements in peripheral acuity and contrast thresholds. The use of this type of this custom video game framework built up from psychophysical approaches takes advantage of the benefits found from video game training while maintaining a tight link to psychophysical designs that enable understanding of mechanisms of perceptual learning and has great potential both as a scientific tool and as therapy to help improve vision.
PMCID: PMC4041814  PMID: 24406157
18.  The response of the amblyopic visual system to noise 
Vision research  2007;47(19):2531-2542.
Visual perception is limited by both the strength of the neural signals, and by the noise in the visual nervous system. Here we use one-dimensional white noise as input, to study the response of amblyopic visual system. We measured the thresholds for detection and discrimination of noise contrast. Using an N-Pass reverse correlation technique, we derived classification images and estimated response consistency.
Our results provide the first report of the sensitivity of the amblyopic visual system to white noise. We show that amblyopes have markedly reduced sensitivity for detecting noise, particularly at high spatial frequencies, and much less loss for discriminating suprathreshold noise contrast. Compensating for the detection loss almost (but not quite) equates performance of the amblyopic and normal visual system.
The classification images suggest that the amblyopic visual system contains adjustable channels for noise, similar to those found in normal vision, but “tuned” to slightly lower spatial frequencies than in normal observers. Our N-pass results show that the predominant factor limiting performance in our task in both normal and amblyopic vision is internal random multiplicative noise. For the detection of white noise the raised thresholds of the amblyopic visual system can be attributed primarily to extra additive noise. However, for the discrimination of suprathreshold white noise contrast, there is surprisingly little additional deficit, after accounting for the visibility of the noise.
PMCID: PMC2099256  PMID: 17697689
white noise; psychophysics; amblyopia; classification images; reverse-correlation; double-pass; internal noise
19.  A double dissociation of the acuity and crowding limits to letter identification, and the promise of improved visual screening 
Journal of Vision  2014;14(5):3.
Here, we systematically explore the size and spacing requirements for identifying a letter among other letters. We measure acuity for flanked and unflanked letters, centrally and peripherally, in normals and amblyopes. We find that acuity, overlap masking, and crowding each demand a minimum size or spacing for readable text. Just measuring flanked and unflanked acuity is enough for our proposed model to predict the observer's threshold size and spacing for letters at any eccentricity.
We also find that amblyopia in adults retains the character of the childhood condition that caused it. Amblyopia is a developmental neural deficit that can occur as a result of either strabismus or anisometropia in childhood. Peripheral viewing during childhood due to strabismus results in amblyopia that is crowding limited, like peripheral vision. Optical blur of one eye during childhood due to anisometropia without strabismus results in amblyopia that is acuity limited, like blurred vision. Furthermore, we find that the spacing:acuity ratio of flanked and unflanked acuity can distinguish strabismic amblyopia from purely anisometropic amblyopia in nearly perfect agreement with lack of stereopsis. A scatter diagram of threshold spacing versus acuity, one point per patient, for several diagnostic groups, reveals the diagnostic power of flanked acuity testing. These results and two demonstrations indicate that the sensitivity of visual screening tests can be improved by using flankers that are more tightly spaced and letter like.
Finally, in concert with Strappini, Pelli, Di Pace, and Martelli (submitted), we jointly report a double dissociation between acuity and crowding. Two clinical conditions—anisometropic amblyopia and apperceptive agnosia—each selectively impair either acuity A or the spacing:acuity ratio S/A, not both. Furthermore, when we specifically estimate crowding, we find a double dissociation between acuity and crowding. Models of human object recognition will need to accommodate this newly discovered independence of acuity and crowding.
PMCID: PMC4021854  PMID: 24799622
amblyopia; crowding; strabismic; anisometropic; acuity; screening; spacing:acuity ratio; critical spacing; threshold spacing; legibility; overlap masking; letter identification; object recognition
20.  Computational refinement of post-translational modifications predicted from tandem mass spectrometry 
Bioinformatics  2011;27(6):797-806.
Motivation: A post-translational modification (PTM) is a chemical modification of a protein that occurs naturally. Many of these modifications, such as phosphorylation, are known to play pivotal roles in the regulation of protein function. Henceforth, PTM perturbations have been linked to diverse diseases like Parkinson's, Alzheimer's, diabetes and cancer. To discover PTMs on a genome-wide scale, there is a recent surge of interest in analyzing tandem mass spectrometry data, and several unrestrictive (so-called ‘blind’) PTM search methods have been reported. However, these approaches are subject to noise in mass measurements and in the predicted modification site (amino acid position) within peptides, which can result in false PTM assignments.
Results: To address these issues, we devised a machine learning algorithm, PTMClust, that can be applied to the output of blind PTM search methods to improve prediction quality, by suppressing noise in the data and clustering peptides with the same underlying modification to form PTM groups. We show that our technique outperforms two standard clustering algorithms on a simulated dataset. Additionally, we show that our algorithm significantly improves sensitivity and specificity when applied to the output of three different blind PTM search engines, SIMS, InsPecT and MODmap. Additionally, PTMClust markedly outperforms another PTM refinement algorithm, PTMFinder. We demonstrate that our technique is able to reduce false PTM assignments, improve overall detection coverage and facilitate novel PTM discovery, including terminus modifications. We applied our technique to a large-scale yeast MS/MS proteome profiling dataset and found numerous known and novel PTMs. Accurately identifying modifications in protein sequences is a critical first step for PTM profiling, and thus our approach may benefit routine proteomic analysis.
Availability: Our algorithm is implemented in Matlab and is freely available for academic use. The software is available online from
Supplementary Information: Supplementary data are available at Bioinformatics online.
PMCID: PMC3051323  PMID: 21258065
21.  Asymmetric Transfer of Auditory Perceptual Learning 
Perceptual skills can improve dramatically even with minimal practice. A major and practical benefit of learning, however, is in transferring the improvement on the trained task to untrained tasks or stimuli, yet the mechanisms underlying this process are still poorly understood. Reduction of internal noise has been proposed as a mechanism of perceptual learning, and while we have evidence that frequency discrimination (FD) learning is due to a reduction of internal noise, the source of that noise was not determined. In this study, we examined whether reducing the noise associated with neural phase locking to tones can explain the observed improvement in behavioral thresholds. We compared FD training between two tone durations (15 and 100 ms) that straddled the temporal integration window of auditory nerve fibers upon which computational modeling of phase locking noise was based. Training on short tones resulted in improved FD on probe tests of both the long and short tones. Training on long tones resulted in improvement only on the long tones. Simulations of FD learning, based on the computational model and on signal detection theory, were compared with the behavioral FD data. We found that improved fidelity of phase locking accurately predicted transfer of learning from short to long tones, but also predicted transfer from long to short tones. The observed lack of transfer from long to short tones suggests the involvement of a second mechanism. Training may have increased the temporal integration window which could not transfer because integration time for the short tone is limited by its duration. Current learning models assume complex relationships between neural populations that represent the trained stimuli. In contrast, we propose that training-induced enhancement of the signal-to-noise ratio offers a parsimonious explanation of learning and transfer that easily accounts for asymmetric transfer of learning.
PMCID: PMC3502074  PMID: 23181045
perceptual learning; transfer of learning; frequency discrimination; internal noise; phase locking; integration time; auditory; modeling
22.  Learning to Identify Near-Acuity Letters, either with or without Flankers, Results in Improved Letter Size and Spacing Limits in Adults with Amblyopia 
PLoS ONE  2012;7(4):e35829.
Amblyopia is a developmental abnormality that results in deficits for a wide range of visual tasks, most notably, the reduced ability to see fine details, the loss in contrast sensitivity especially for small objects and the difficulty in seeing objects in clutter (crowding). The primary goal of this study was to evaluate whether crowding can be ameliorated in adults with amblyopia through perceptual learning using a flanked letter identification task that was designed to reduce crowding, and if so, whether the improvements transfer to untrained visual functions: visual acuity, contrast sensitivity and the size of visual span (the amount of information obtained in one fixation). To evaluate whether the improvements following this training task were specific to training with flankers, we also trained another group of adult observers with amblyopia using a single letter identification task that was designed to improve letter contrast sensitivity, not crowding. Following 10,000 trials of training, both groups of observers showed improvements in the respective training task. The improvements generalized to improved visual acuity, letter contrast sensitivity, size of the visual span, and reduced crowding. The magnitude of the improvement for each of these measurements was similar in the two training groups. Perceptual learning regimens aimed at reducing crowding or improving letter contrast sensitivity are both effective in improving visual acuity, contrast sensitivity for near-acuity objects and reducing the crowding effect, and could be useful as a clinical treatment for amblyopia.
PMCID: PMC3340394  PMID: 22558234
23.  Using visual noise to characterize amblyopic letter identification 
Journal of vision  2004;4(10):904-920.
Amblyopia is a much-studied but poorly understood developmental visual disorder that reduces acuity, profoundly reducing contrast sensitivity for small targets. Here we use visual noise to probe the letter identification process and characterize its impairment by amblyopia. We apply five levels of analysis — threshold, threshold in noise, equivalent noise, optical MTF, and noise modeling — to obtain a two-factor model of the amblyopic deficit: substantially reduced efficiency for small letters and negligibly increased cortical noise. Cortical noise, expressed as an equivalent input noise, varies among amblyopes but is roughly 1.4× normal, as though only 1/1.4 the normal number of cortical spikes are devoted to the amblyopic eye. This raises threshold contrast for large letters by a factor of √1.4 = 1.2×, a negligible effect. All 16 amblyopic observers showed near-normal efficiency for large letters (> 4× acuity) and greatly reduced efficiency for small letters: 1/4 normal at 2× acuity and approaching 1/16 normal at acuity. Finding that the acuity loss represents a loss of efficiency rules out all models of amblyopia except those that predict the same sensitivity loss on blank and noisy backgrounds. One such model is the last-channel hypothesis, which supposes that the highest-spatial-frequency channels are missing, leaving the remaining highest-frequency channel struggling to identify the smallest letters. However, this hypothesis is rejected by critical band masking of letter identification, which shows that the channels used by the amblyopic eye have normal tuning for even the smallest letters. Finally, based on these results, we introduce a new “Dual Acuity” chart that promises to be a quick diagnostic test for amblyopia.
PMCID: PMC2751822  PMID: 15595894
amblyopia; noise; efficiency; cortical noise; Pelli-Levi Dual Acuity Chart
24.  Metamorphopsia and letter recognition 
Journal of Vision  2014;14(14):1.
Acuity is the most commonly used measure of visual function, and reductions in acuity are associated with most eye diseases. Metamorphopsia—a perceived distortion of visual space—is another common symptom of visual impairment and is currently assessed qualitatively using Amsler (1953) charts. In order to quantify the impact of metamorphopsia on acuity, we measured the effect of physical spatial distortion on letter recognition. Following earlier work showing that letter recognition is tuned to specific spatial frequency (SF) channels, we hypothesized that the effect of distortion might depend on the spatial scale of visual distortion just as it depends on the spatial scale of masking noise. Six normally sighted observers completed a 26 alternate forced choice (AFC) Sloan letter identification task at five different viewing distances, and the letters underwent different levels of spatial distortion. Distortion was controlled using spatially band-pass filtered noise that spatially remapped pixel locations. Noise was varied over five spatial frequencies and five magnitudes. Performance was modeled with logistic regression and worsened linearly with increasing distortion magnitude and decreasing letter size. We found that retinal SF affects distortion at midrange frequencies and can be explained with the tuning of a basic contrast sensitivity function, while object-centered distortion SF follows a similar pattern of letter object recognition sensitivity and is tuned to approximately three cycles per letter (CPL). The interaction between letter size and distortion makes acuity an unreliable outcome for metamorphopsia assessment.
PMCID: PMC4249589  PMID: 25453116
letter recognition; visual acuity; spatial vision; metamorphopsia; clinical vision; macular degeneration
25.  Involuntary attention enhances identification accuracy for unmasked low contrast letters using non-predictive peripheral cues 
Vision research  2013;89:10.1016/j.visres.2013.06.010.
There is controversy regarding whether or not involuntary attention improves response accuracy at a cued location when the cue is non-predictive and if these cueing effects are dependent on backward masking. Various perceptual and decisional mechanisms of performance enhancement have been proposed, such as signal enhancement, noise reduction, spatial uncertainty reduction, and decisional processes. Herein we review a recent report of mask-dependent accuracy improvements with low contrast stimuli and demonstrate that the experiments contained stimulus artifacts whereby the cue impaired perception of low contrast stimuli, leading to an absence of improved response accuracy with unmasked stimuli. Our experiments corrected these artifacts by implementing an isoluminant cue and increasing its distance relative to the targets. The results demonstrate that cueing effects are robust for unmasked stimuli presented in the periphery, resolving some of the controversy concerning cueing enhancement effects from involuntary attention and mask dependency. Unmasked low contrast and/or short duration stimuli as implemented in these experiments may have a short enough iconic decay that the visual system functions similarly as if a mask were present leading to improved accuracy with a valid cue.
PMCID: PMC3813696  PMID: 23872240

Results 1-25 (1140849)