Segmenting surface boundaries using luminance cues.
Ontology highlight
ABSTRACT:
SUBMITTER: DiMattina C
PROVIDER: S-EPMC8115076 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The accurate segmentation of the brain surface in post-surgical computed tomography (CT) images is critical for image-guided neurosurgical procedures in epilepsy patients. Following surgical implantation of intracranial electrodes, surgeons require accurate registration of the post-implantation CT images to the pre-implantation functional and structural magnetic resonance imaging to guide surgical resection of epileptic tissue. One way to perform the registration is via surface matching. The key challenge in this setup is the CT segmentation, where the extraction of the cortical surface is difficult due to the missing parts of the skull and artifacts introduced from the electrodes. In this paper, we present a dictionary learning-based method to segment the brain surface in post-surgical CT images of epilepsy patients following surgical implantation of electrodes. We propose learning a model of locally oriented appearance that captures both the normal tissue and the artifacts found along this brain surface boundary. Utilizing a database of clinical epilepsy imaging data to train and test our approach, we demonstrate that our method using locally oriented image appearance both more accurately extracts the brain surface and better localizes electrodes on the post-operative brain surface compared to standard, non-oriented appearance modeling. In addition, we compare our method to a standard atlas-based segmentation approach and to a U-Net-based deep convolutional neural network segmentation method.
| S-EPMC6476428 | biostudies-literature
Project description:BackgroundNumerosity estimation is a basic preverbal ability that humans share with many animal species and that is believed to be foundational of numeracy skills. It is notoriously difficult, however, to establish whether numerosity estimation is based on numerosity itself, or on one or more non-numerical cues like-in visual stimuli-spatial extent and density. Frequently, different non-numerical cues are held constant on different trials. This strategy, however, still allows numerosity estimation to be based on a combination of non-numerical cues rather than on any particular one by itself.Methodology/principal findingsHere we introduce a novel method, based on second-order (contrast-based) visual motion, to create stimuli that exclude all first-order (luminance-based) cues to numerosity. We show that numerosities can be estimated almost as well in second-order motion as in first-order motion.Conclusions/significanceThe results show that numerosity estimation need not be based on first-order spatial filtering, first-order density perception, or any other processing of luminance-based cues to numerosity. Our method can be used as an effective tool to control non-numerical variables in studies of numerosity estimation.
| S-EPMC3046164 | biostudies-literature
Project description:Theory predicts that colour polymorphism may be favored by variation in the visual context under which signals are perceived. The context encompasses all environmental determinants of light availability and propagation, but also the dynamics of perception in receivers. Color vision involves the neural separation of information into spectral versus luminance channels, which often differentially guide specific tasks. Here we explicitly tested whether this discrete perceptual basis contributes to the maintenance of polymorphism in a prey-luring system. The orb-weaving spider Gasteracantha fornicata is known to attract a broad community of primarily dipteran prey due to their conspicuous banded dorsal signal. They occur in two morphs ("white" and "yellow") which should, respectively, generate greater luminance and color contrast in the dipteran eye. Given that arthropods often rely upon luminance-versus-spectral cues for relatively small-versus-large stimulus detection, we predicted a switch in relative attractiveness among morphs according to apparent spider size.Our experimental tests used colour-naïve individuals of two known prey species (Drosophila hydei and Musca domestica) in replicate Y-maze choice trials designed to manipulate the apparent size of spider models via the distance at which they are viewed. Initial trials confirmed that flies were attracted to each G. fornicata morph in single presentations. When given a simultaneous choice between morphs against a viewing background typical of those encountered in nature, flies exhibited no preference regardless of the visual angle subtended by models. However, when backgrounds were adjusted to nearer the extremes of those of each morph in the wild, flies were more attracted by white morphs when presented at longer range (consistent with a reliance on achromatic cues), yet were unbiased in their close-range choice.While not fully consistent with predictions (given the absence of a differential preference for stimuli at close range), our results demonstrate an effect of apparent stimulus size upon relative morph attractiveness in the direction anticipated from present knowledge of fly visual ecology. This implies the potential tuning of G. fornicata morph signal structure according to a perceptual feature that is likely common across their breadth of arthropod prey, and complements recent observational work in suggesting a candidate mechanism for the maintenance of deceptive polymorphism through the exploitation of different visual channels in prey.
| S-EPMC5557064 | biostudies-literature
Project description:Our visual system ably integrates the visible parts of a partially occluded surface with the occluded parts (amodal surface completion), mainly by relying on the surface boundary contours of the image. Less known, is whether the visual system also utilizes surface feature information, such as luminance contrast polarity, for surface completion. We conducted three experiments to investigate this issue. Experiment 1 found that when visible segments of a partially occluded rectangle with the same luminance contrast polarity move behind an occluding surface, observers perceive the visible segments as part of the occluded rectangle moving cohesively behind the occluding surface. However, when the visible segments have opposite luminance contrast polarity, the global motion of the segments is barely perceived, suggesting a failure of amodal surface integration. Experiment 2 revealed that this same luminance contrast polarity constraint applies to amodal surface integration of a display without an explicit occluding surface image. Experiment 3 showed that both the shape and luminance contrast polarity of the visible segments of the partially occluded rectangle affect amodal surface completion. Together, these findings demonstrate that luminance contrast polarity, along with surface boundary contour, are important cues for amodal surface integration.
| S-EPMC7694893 | biostudies-literature
Project description:Boundary formation in the developing neuroepithelium decides on the position and size of compartments in the adult nervous system. In this study, we start from the French Flag model proposed by Lewis Wolpert, in which boundaries are formed through the combination of morphogen diffusion and of thresholds in cell responses. In contemporary terms, a response is characterized by the expression of cell-autonomous transcription factors, very often of the homeoprotein family. Theoretical studies suggest that this sole mechanism results in the formation of boundaries of imprecise shapes and positions. Alan Turing, on the other hand, proposed a model whereby two morphogens that exhibit self-activation and reciprocal inhibition, and are uniformly distributed and diffuse at different rates lead to the formation of territories of unpredictable shapes and positions but with sharp boundaries (the 'leopard spots'). Here, we have combined the two models and compared the stability of boundaries when the hypothesis of local homeoprotein intercellular diffusion is, or is not, introduced in the equations. We find that the addition of homeoprotein local diffusion leads to a dramatic stabilization of the positioning of the boundary, even when other parameters are significantly modified. This novel Turing/Wolpert combined model has thus important theoretical consequences for our understanding of the role of the intercellular diffusion of homeoproteins in the developmental robustness of and the changes that take place in the course of evolution.
| S-EPMC5207310 | biostudies-literature
Project description:The unique ability to identify one's own body and experience it as one's own is fundamental in goal-oriented behavior and survival. However, the mechanisms underlying the so-called body ownership are yet not fully understood. Evidence based on Rubber Hand Illusion (RHI) paradigms has demonstrated that body ownership is a product of reception and integration of self and externally generated multisensory information, feedforward and feedback processing of sensorimotor signals, and prior knowledge about the body. Crucially, however, these designs commonly involve the processing of proximal modalities while the contribution of distal sensory signals to the experience of ownership remains elusive. Here we propose that, like any robust percept, body ownership depends on the integration and prediction across all sensory modalities, including distal sensory signals pertaining to the environment. To test our hypothesis, we created an embodied goal-oriented Virtual Air Hockey Task, in which participants were to hit a virtual puck into a goal. In two conditions, we manipulated the congruency of distal multisensory cues (auditory and visual) while preserving proximal and action-driven signals entirely predictable. Compared to a fully congruent condition, our results revealed a significant decrease on three dimensions of ownership evaluation when distal signals were incongruent, including the subjective report as well as physiological and kinematic responses to an unexpected threat. Together, these findings support the notion that the way we represent our body is contingent upon all the sensory stimuli, including distal and action-independent signals. The present data extend the current framework of body ownership and may also find applications in rehabilitation scenarios.
| S-EPMC8551865 | biostudies-literature
Project description:In this work, we propose a novel cascaded V-Nets method to segment brain tumor substructures in multimodal brain magnetic resonance imaging. Although V-Net has been successfully used in many segmentation tasks, we demonstrate that its performance could be further enhanced by using a cascaded structure and ensemble strategy. Briefly, our baseline V-Net consists of four levels with encoding and decoding paths and intra- and inter-path skip connections. Focal loss is chosen to improve performance on hard samples as well as balance the positive and negative samples. We further propose three preprocessing pipelines for multimodal magnetic resonance images to train different models. By ensembling the segmentation probability maps obtained from these models, segmentation result is further improved. In other hand, we propose to segment the whole tumor first, and then divide it into tumor necrosis, edema, and enhancing tumor. Experimental results on BraTS 2018 online validation set achieve average Dice scores of 0.9048, 0.8364, and 0.7748 for whole tumor, tumor core and enhancing tumor, respectively. The corresponding values for BraTS 2018 online testing set are 0.8761, 0.7953, and 0.7364, respectively. We also evaluate the proposed method in two additional data sets from local hospitals comprising of 28 and 28 subjects, and the best results are 0.8635, 0.8036, and 0.7217, respectively. We further make a prediction of patient overall survival by ensembling multiple classifiers for long, mid and short groups, and achieve accuracy of 0.519, mean square error of 367240 and Spearman correlation coefficient of 0.168 for BraTS 2018 online testing set.
| S-EPMC7033427 | biostudies-literature
Project description:The cognitive map is often assumed to be a Euclidean map that isometrically represents the real world (i.e., the Euclidean distance between any two locations in the physical world should be preserved on the cognitive map). However, accumulating evidence suggests that environmental boundaries can distort the mental representations of physical space. For example, the distance between two locations can be remembered as longer than the true physical distance if the locations are separated by a boundary. While this overestimation is observed under different experimental conditions, even when the boundary is formed by flat surface cues, its physiological basis is not well understood. We examined the neural representation of flat surface cue boundaries, and of the space segregated by these boundaries, by recording place cell activity from CA1 and CA3 while rats foraged on a circular track or square platforms with inhomogeneous surface textures. About 40% of the place field edges concentrated near the boundaries on the circular track (significantly above the chance level 33%). Similarly, place field edges were more prevalent near boundaries on the platforms than expected by chance. In both one- and two-dimensional environments, the population vectors of place cell activity changed more abruptly with distance between locations that crossed cue boundaries than between locations within a bounded region. These results show that the locations of surface boundaries were evident as enhanced decorrelations of the neural representations of locations to either side of the boundaries. This enhancement might underlie the cognitive phenomenon of overestimation of distances across boundaries.
| S-EPMC7259364 | biostudies-literature
Project description:Wiring the nervous system relies on the interplay of intrinsic and extrinsic signaling molecules that control neurite extension, neuronal polarity, process maturation and experience-dependent refinement. Extrinsic signals establish and enrich neuron-neuron interactions during development. Understanding how such extrinsic cues direct neurons to establish neural connections in vitro will facilitate the development of organized neural networks for investigating the development and function of nervous system networks. Producing ordered networks of neurons with defined connectivity in vitro presents special technical challenges because the results must be compliant with the biological requirements of rewiring neural networks. Here we demonstrate the ability to form stable, instructive surface-bound gradients of laminin that guide postnatal hippocampal neuron development in vitro. Our work uses a three-channel, interconnected microfluidic device that permits the production of adlayers of planar substrates through the combination of laminar flow, diffusion and physisorption. Through simple flow modifications, a variety of patterns and gradients of laminin (LN) and fluorescein isothiocyanate-conjugated poly-l-lysine (FITC-PLL) were deposited to present neurons with an instructive substratum to guide neuronal development. We present three variations in substrate design that produce distinct growth regimens for postnatal neurons in dispersed cell cultures. In the first approach, diffusion-mediated gradients of LN were formed on cover slips to guide neurons toward increasing LN concentrations. In the second approach, a combined gradient of LN and FITC-PLL was produced using aspiration-driven laminar flow to restrict neuronal growth to a 15 microm wide growth zone at the center of the two superimposed gradients. The last approach demonstrates the capacity to combine binary lines of FITC-PLL in conjunction with surface gradients of LN and bovine serum albumin (BSA) to produce substrate adlayers that provide additional levels of control over growth. This work demonstrates the advantages of spatio-temporal fluid control for patterning surface-bound gradients using a simple microfluidics-based substrate deposition procedure. We anticipate that this microfluidics-based patterning approach will provide instructive patterns and surface-bound gradients to enable a new level of control in guiding neuron development and network formation.
| S-EPMC2930779 | biostudies-literature
Project description:BackgroundWe evaluated the reproducibility of office-based flicker electroretinography (ERG) in patients with nonproliferative diabetic retinopathy (NPDR).MethodsAn observational study was conducted in which ultra-widefield fluorescein angiography (UWF-FA) was performed on 20 patients with mild-to-moderate NPDR; images were graded by the Fundus Photography Reading Center (Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI, USA). Fixed- and multi-luminance flicker ERG was repeated four times (greater than or equal to seven days apart). Recording consistency was assessed using intra-class correlation coefficients (ICCs), coefficients of variation, and Pearson correlations.Results82.5% and 17.5% of eyes had mild and moderate NPDR using UWF-FA; 90% of the angiograms were given a high confidence grade. Fixed-luminance phase values were highly reproducible (ICC: 0.949; P < .001). There was a significant negative correlation between fixed-luminance phase and log-corrected ischemic index values (-0.426; P = .015).ConclusionsOffice-based, fixed-luminance phase values are highly reproducible and negatively correlate with retinal ischemia in NPDR, suggesting that global retinal dysfunction may be reliably quantified early in patients with diabetes.
| S-EPMC7645135 | biostudies-literature