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Statistical shape analysis: clustering, learning, and testing.

Using a differential-geometric treatment of planar shapes, we present tools for: 1) hierarchical clustering of imaged objects according to the shapes of their boundaries, 2) learning of probability models for clusters of shapes, and 3) testing of newly observed shapes under competing probability models. Clustering at any level of hierarchy is performed using a mimimum variance type criterion criterion and a Markov process. Statistical means of clusters provide shapes to be clustered at the next higher level, thus building a hierarchy of shapes. Using finite-dimensional approximations of spaces tangent to the shape space at sample means, we (implicitly) impose probability models on the shape space, and results are illustrated via random sampling and classification (hypothesis testing). Together, hierarchical clustering and hypothesis testing provide an efficient framework for shape retrieval. Examples are presented using shapes and images from ETH, Surrey, and AMCOM databases.

Algorithms↗

Shape classification using the inner-distance.

Part structure and articulation are of fundamental importance in computer and human vision. We propose using the inner-distance to build shape descriptors that are robust to articulation and capture part structure. The inner-distance is defined as the length of the shortest path between landmark points within the shape silhouette. We show that it is articulation insensitive and more effective at capturing part structures than the Euclidean distance. This suggests that the inner-distance can be used as a replacement for the Euclidean distance to build more accurate descriptors for complex shapes, especially for those with articulated parts. In addition, texture information along the shortest path can be used to further improve shape classification. With this idea, we propose three approaches to using the inner-distance. The first method combines the inner-distance and multidimensional scaling (MDS) to build articulation invariant signatures for articulated shapes. The second method uses the inner-distance to build a new shape descriptor based on shape contexts. The third one extends the second one by considering the texture information along shortest paths. The proposed approaches have been tested on a variety of shape databases, including an articulated shape data set, MPEG7 CE-Shape-1, Kimia silhouettes, the ETH-80 data set, two leaf data sets, and a human motion silhouette data set. In all the experiments, our methods demonstrate effective performance compared with other algorithms.

Algorithms↗

Relationships of age and shape of the navicular bone to the development of navicular disease: a radiological study.

Estimating the shape of the proximal articular border of the navicular bone and grading the radiological navicular bone condition (grades 3 and 4 representing the most severe changes), the aim of this study was to assess potential age-related implications of the previously reported shape predisposition to navicular disease in 746 normal and 174 clinically affected Dutch Warmbloods age 3-19 years. A significant, age-independent, shape-grade association found in normal and affected horses emphasises the fundamental character of the shape predisposition to navicular disease. A significant age-related increase of the least susceptible shape prevalence was found in elderly normal horses. A shape-independent low grades 3 and 4 prevalence (mean 15%) was found in normal horses, vs. a high grades 3 and 4 prevalence (mean 85%) in the affected horses. Therefore, the clinical manifestation of the disease is grade-rather than shape-dependent. A significant age-related appearance of inverted flask-shaped channels and enthesophytes was found in the clinically affected horses. However, considering the significant shape-radiological features association previously reported in 3-year-old normal horses, this association may be shape- rather than age-dependent.

Animals↗

Observations on the change in shape of blood platelets brought about by adenosine diphosphate.

1. An optical method used for measuring platelet aggregation was adapted for measurements of the change in shape of platelets that rapidly follows the addition of the aggregating agent adenosine diphosphate (ADP).2. Measurements were made using dilute suspension of platelets with sufficient EDTA to prevent their aggregation.3. Measurements of the velocity and magnitude of the optical effects of the shape change were highly reproducible.4. Volumetric measurements showed that the shape change is not associated with an increase in mean platelet volume.5. The velocity of the shape change had a temperature coefficient of about 4.5.6. The velocity and magnitude of the shape change were not affected by pH between 5.8 and 9.2.7. The dependence of the velocity of the shape change on the ADP concentration was in accordance with Michaelis-Menton kinetics. The K(m) was about 7.2 x 10(-7)M.8. The velocity of the shape change was inhibited competitively by ATP, adenosine and 2-chloroadenosine but not by AMP. When the inhibitors were added after the maximum of the shape change they caused a concentration-dependent diminution in the record of the change.9. The results suggest that the shape change is initiated by reaction of the agonist ADP with specific receptor sites on the platelet membrane which leads to energy-requiring changes in the structures responsible for maintaining the disk shape of normal platelets.

Adenine Nucleotides↗

The role of the gross spectral shape as a perceptual cue to place articulation in initial stop consonants.

This series of studies explored the extent to which the gross shape of the onset spectrum is used by the listener for the identification of place of articulation in initial stop consonants. Synthetic stimuli were generated with onset frequencies appropriate to the syllables [ba bi du da di du] and with the gross shape of the onset spectrum manipulated to be appropriate for either alveolar consonants or labial consonants. Stimuli were presented for identification and discrimination. In addition, adaptation effects of stimuli containing appropriate frequency and shape and incompatible frequency and shape were explored on a place-of-articulation onset continuum. Although identification performance was determined by onset frequency rather than gross shape of the spectrum, presentation of stimuli in which shape was inconsistent with frequency reduced identification performance. Further, subjects could discriminate stimuli which varied only in spectral shape. Finally, significantly less adaptation was found for a [da] onset with a labial spectrum shape than [da] onset with an alveolar spectrum shape. These results suggest that although the invariant properties residing in the gross shape of the onset spectrum may serve as a classificatory framework for the phonetic dimensions of natural language, they may not provide the primary perceptual attributes for place of articulation in ongoing speech processing.

Humans↗

The effect of contour closure on shape perception.

We studied psychophysically whether 'contour closure' enhances the accuracy of shape perception. Stimulus configurations (presented on a blank background) always consisted of identical pattern elements, but the positions of the local elements were varied: the global contour shape either contained closure or not. In the first two stimulus conditions (Closure), the oriented pattern elements (Gabor patches) formed a 'closed' rectangular shape composed of either four long lines or four corners. In the third condition (No closure), the global shape was composed of the four corners, but they were outward oriented, and hence they did not form the outline of a closed contour. We measured the precision of shape perception using a discrimination task in which observers judged the aspect ratio of the outline shape i.e. whether the rectangular shape was tall or wide. We found that: (i) shape discrimination was better (more precise) for Closed contours than for Non-closed contours, i.e. the aspect ratio discrimination thresholds were lower for the Closed than Non-closed configurations. The improved performance could not be explained by differences in visibility of the local elements in the two conditions. (ii) For closed contours, shape discrimination was more precise when the local elements were aligned with the global shape, than when the local elements were orthogonal to it.

Form Perception↗

Perceived orientation of complex shape reflects graded part decomposition.

Although the orientation of line segments and simple shapes is a well-studied area of vision, little is known about geometric factors that influence perceived orientation of complex multipart shapes. The study of these factors is of interest because it allows for an insight into the basic problem of how local geometric attributes are integrated perceptually into a global shape representation. We examined the perceived orientation of two-part shapes using an adjustment method and a 2AFC task. In particular, we investigated the influence of the perceptual salience, or distinctiveness, of a part--as defined by the turning angles at its boundaries--and its area relative to the main "base" part. In contrast to previous results on simple shapes, our results exhibited large and systematic deviations of perceived orientation from the principal axis of the shape. For shapes with sharp part boundaries, perceived global orientation deviated maximally from the principal axis and was approximated by the axis of the main base part of the shape. With weakening part boundaries, the perceived orientation gradually approached the principal axis of the entire shape, reflecting that both parts were taken into account in estimating orientation. The results are consistent with a differentially weighted principal-axis computation in which the attached part is given systematically lower weighting with increasing turning angles at the part boundaries. They thus allow a quantitative characterization of part salience in terms of part independence: Turning angles at a part's boundaries determine the extent to which its influence is perceptually separable from the rest of the shape. We suggest that Robust Statistics may provide a useful framework for quantifying the influence of part segmentation on visual estimation.

Adult↗

Thought-shape fusion in eating disorders.

OBJECTIVES: The aims of the present study were (1) to examine the association between a cognitive distortion ('thought-shape fusion') and eating disorder psychopathology and (2) to examine the degree of thought-shape fusion in people with eating disorders and a non-eating-disorder control group. DESIGN: Associations between thought-shape fusion and eating disorder psychopathology were examined and the degree of thought-shape fusion was compared between people with and without clinical eating disorders. METHOD: Forty-two women with clinical eating disorders and a group of 42 age-matched women with no self-reported history of an eating disorder completed self-report questionnaires to assess thought-shape fusion, eating disorder symptoms, body checking and body avoidance, and depression. RESULTS: Thought-shape fusion was significantly associated with eating disorder psychopathology. The majority of the associations remained significant when controlling for levels of depression. Patients with eating disorders showed significantly more thought-shape fusion than the non-clinical controls. CONCLUSIONS: Thought-shape fusion is a cognitive distortion associated with eating disorders. It may be a direct expression of the overevaluation of eating, shape and weight. It is recommended that thought-shape fusion be tackled directly in cases where it is a barrier to changing the core psychopathology of eating disorders.

Adolescent↗

Blastula wall invagination examined on the basis of shape behavior of vesicular objects with laminar envelopes.

A complete description of the blastula shape transformations which occur in the process of gastrulation involves the mechanics of the blastula wall. It is inferred that the mechanical properties of this wall can, to a first approximation, be described in terms of elastic deformational modes which are equivalent to those of simple vesicular systems such as phospholipid vesicles and red blood cells. For membranes composed of an arbitrary number of aligned, laterally unconnected thin layers, these are area expansivity and local and non-local bending. Stable shapes of vesicular objects with laminar envelopes are defined as shapes which correspond to the minimum of the system elastic energy. The shape behavior of these objects is briefly reported. The criterion for the stability of the spherical shape of a vesicular object is derived. In particular we analyze the shape transition from a sphere to an invaginated gastrula. Conditions are demonstrated under which this shape transition can occur through a series of continuous shape transformations. A possible example of such a shape transformation is given. The blastula wall of the sea urchin is modeled as a closed laminar membranous system with three layers, the monocellular epithelial sheet and the extracellular apical lamina and hyaline layers. Experimentally measured elastic constants of some of these layers are shown to be in accord with the restrictions on their values imposed by the requirement for continuous shape transformations.

Animals↗

Assessing the shape of the glucose curve during an oral glucose tolerance test.

OBJECTIVE: The oral glucose tolerance test (OGTT) is used to define the status of glucose tolerance based on the plasma glucose level at 120 min. The purpose of the present study was to identify parameters that determine the shape of the plasma glucose course measured at 0, 30, 60, 90, and 120 min during an OGTT. RESEARCH DESIGN AND METHODS: OGTT data from 551 subjects (485 with normal glucose tolerance [NGT] and 66 with impaired glucose tolerance [IGT]) were analyzed. We distinguished between "monophasic," "biphasic," and unclassified glucose shapes. A "shape" index based on the extent and the direction of the plasma glucose change in the second hour allowed us to treat shape as a continuous variable. RESULTS: In the biphasic group, the NGT-to-IGT ratio was slightly higher (173/20 vs. 209/40, P = 0.08) and the male-to-female ratio was lower (60/133 vs. 120/129, P = 0.0003). Subjects with a biphasic shape had significantly lower age, BMI, waist-to-hip ratio (WHR), HbA(1c), plasma glucose, and area under the insulin curve (insulin(AUC)) and a better estimated insulin sensitivity and secretion (using validated indexes) than monophasic subjects (all P < 0.05). By adjusting this shape index for glucose(AUC) (as continuous measure of glucose tolerance), correlations with age, BMI, WHR, HbA(1c), and insulin(AUC) were completely abolished. The adjusted shape index was still higher in female than in male subjects but lower in IGT than in NGT subjects (both P = 0.0003). Finally, we tested common polymorphisms in insulin receptor substrate (IRS)-1, IRS-2, calpain-10, hepatic lipase, and peroxisome proliferator-activated receptor-gamma for association with the shape index. CONCLUSIONS: We conclude that the plasma glucose shape during an OGTT depends on glucose tolerance and sex. In addition, genetic factors seem to play a role. The shape index may be a useful metabolic screening parameter in epidemiological and genetic association studies.

Administration, Oral↗

The organization of multidimensional selection on the basis of color and shape: an event-related brain potential study.

In this paper, we examine whether color and shape, tied to a single object in space, (1) are identified and selected in series or in parallel, (2) are identified and selected in a dependent, self-terminating manner or in an independent and exhaustive manner, and (3) are conjoined by a feature integration process before or only after an initial stage of separate attribute analyses has finished. We measured response time and the selection negativity (SN) derived from event-related brain potentials when participants responded to a unique conjunction of color and shape in a go/no-go target detection task. The discriminability of the color and the shape of the conjunction was manipulated in three conditions. When color and shape were easy to discriminate, the SNs to color and shape started at the same time. When one attribute was less discriminable the SN to that attribute started later, but not the SN to the complementary attribute. This suggests that color and shape are identified and selected in parallel. In all three discriminability conditions, the SNs to color and shape were initially independent but later interacted. This suggests that color and shape are initially selected independently and exhaustively, after which their conjunction is analyzed. The SN to local shape features started later than that to the conjunction of color and global shape features, which suggests that feature integration can start before the analyses of the separate attributes have finished.

Adult↗

Shape constancy from novel views.

Prior experiments on shape constancy from novel views are inconclusive: Some show that shapes of objects can be recognized reliably from novel views, whereas others show just the opposite. Our analysis of prior results suggests that shape constancy from novel views is reliable when the object has properties that constrain its shape: The object has volumetric primitives, it has surfaces, it is symmetrical, it is composed of geons, its contours are planar, and its images provide useful topological information about its three-dimensional structure. To test the role of some of these constraints, we performed a set of experiments. Solid shapes (polyhedra) were shown on a computer monitor by means of kinetic depth effect. Experiment 1 showed that shape constancy can be reliably achieved when a polyhedron is represented by its contours (most of the constraints are present), but not when it is represented by vertices or by a polygonal line connecting the vertices in a random order (all the constraints are absent). Experiments 2 and 3 tested the role of individual constraints. Results of these experiments show that shape constancy from novel views is reliable when the object has planar contours and when the shapes of the contours together with topological information about the relations among the contours constrain the possible interpretations of the shape. Symmetry of the object and the topological stability of its image also contribute to shape constancy.

Form Perception↗

Discrimination of 3-D shape and 3-D curvature from motion in active vision.

We examined the ability of human observers to discriminate between different 3-D quadratic surfaces defined by motion, and with head position fed back to the stimulus to provide an up-to-date dynamical perspective view. We tested whether 3-D shape or 3-D curvature would affect discrimination performance. It appeared that discrimination of 3-D quadratic shape clearly depended on shape but not on the amount of curvature. Even when the amount of curvature was randomized, subjects' performance was not altered. On the other hand, the discrimination of 3-D curvature clearly depended linearly on curvature with Weber fractions of 20% on the average and, to a small degree, on 3-D shape. The experiment shows that observers can easily separate 3-D shape and 3-D curvature, and that Koenderink's shape index and curvedness provide a convenient way to specify shape. These results warn us against using just any arbitrary 3-D shape in 3-D shape perception tasks and indicate, for example, that emphasizing 3-D shape in computer displays by exaggerating curvature does not have any effect.

Discrimination Learning↗

[Development of a new method for diagnosing the origin of urinary bleeding by doghnut-shape urinary red blood cells].

Although the presence of acanthocytes (AC) is a reliable indicator of glomerular bleeding, acanthocytes could be observed in only 60% of patients with glomerulonephritis. Therefore, we attempted to develop a new method for diagnosing the origin of urinary bleeding by the morphological characteristics of doughnut-shaped of urinary red blood cells (RBC). In the present study, urine samples from 7 patients with glomerular bleeding and 4 patients with non-glomerular bleeding, and from 35 urine samples of the glomerular bleeding and non-glomerular bleeding-model were examined. The various type of RBC were observed by a phase contrast microscopic examination. The doughnut-shaped RBC were divided into three shapes (namely, smooth, uneven, target-shaped RBC) by individual characteristics. The appearance rate of each shape was calculated, and both outer and inner diameters of doughnut-shaped RBC in the photographs were also measured. Although there was no change in the value of outer diameter of doughnut-shaped RBC between glomerular bleeding and non-glomerular bleeding, the values of inner diameter of doughnut-shaped RBC in non-glomerular bleeding was significantly smaller than those in glomerular bleeding in all shapes. These results strongly suggested that the measurement of inner diameters of doughnut-shaped RBC is one of the useful diagnostic methods to distinguish the origin of urinary bleeding when AC could not be observed.

Erythrocytes, Abnormal↗

Space-time clusters with flexible shapes.

INTRODUCTION: Detection of space-time clusters plays an important role in epidemiology and public health. Different approaches for detecting space-time clusters have been proposed and implemented. Many of these approaches are based on the spatial scan statistic formulation. One key aspect of these cluster detection methods is the choice of cluster shape. OBJECTIVES: In this report, the effect of using flexible shapes for clusters is explored by discussing the issues that need to be considered and evaluated. METHODS: The first issue is the flexibility of the shape and its ability to model the disease cluster being studied. Another subtle and related factor is that with a more flexible shape, clusters can appear more often by chance, which will be reflected in the p value obtained through Monte Carlo hypothesis testing. Choosing more complex cluster shapes can affect the computational requirements and also constrain the cluster detection approaches that could be applied. RESULTS: The New Mexico brain cancer data set is used to illustrate the tradeoffs. The analysis of these data should not be construed as a comprehensive investigation from the public health perspective. The data set is used to illustrate and compare clusters with two different shapes, cylinder and square pyramid. The results indicate the insights that can be gained from these shapes, individually and collectively. CONCLUSION: The domain expert should choose the cluster shape, being aware of the disease being modeled and the analysis goals. For example, a flexible shape like the square pyramid can model either growth or shrinkage and movement of the disease and might provide insights on its origin. In addition, performing the analyses with more than one shape can lead to increased insights regarding the disease cluster.

Brain Neoplasms↗

Delineation of the various shapes and patterns of nevi.

It has been proposed that all nevi reflect mosaicism, and this concept has been corroborated at the molecular level in a number of nevi. If the concept of mosaicism holds true, one would expect that the various types of nevi should be characterized by intrinsic shapes or patterns. A photographic review of 1,188 recognizable images of a list of nevi of the skin was undertaken in order to delineate a classification of the various shapes and patterns of nevi. We disclosed three distinct shapes and two so far undescribed archetypical patterns, in addition to the well-known Blaschko-linear, flag-like and extensive garment-like patterns, to which all lesions could be allocated. The newly delineated shapes are called round or oval shape; patches with indented borders; and teardrop or triangular shape. The newly proposed archetypical configurations are the agminated pattern and the diffuse patchy pattern. Other mosaic patterns, such as the phylloid pattern or the lateralization pattern, were not observed in any of the images reviewed. We conclude that the various types of nevi can be assigned to specific shapes or patterns. Admittedly, however, a given nevus may manifest itself in several different shapes, whereas its archetypical pattern tends to be the same. This 'archetypical' pattern can be taken as the perfect or ideal model of a given type of nevus, whereas the newly described shapes are subordinated to the archetypical patterns and are best considered to be 'nonarchetypical'. Our work gives more consistency to the idea that nevi reflect mosaicism, because they display repetitive shapes and patterns.

Child↗

Morphometric analyses of changes in cell shape in the neuroepithelium of mammalian embryos.

During neurulation the elevation of the neural folds is accompanied by, and thought to be partly driven by, changes in the shapes of the neuroepithelial cells. This paper explores the use of form factors for the measurement of changes in cell shape during normal and perturbed neural fold elevation in rat embryos; it is the first attempt to quantify changes in the shapes of cells during neurulation in mammalian embryos. Rat embryos at 9.9 days of gestation, when the neural epithelium is a biconvex plate, and at 10.4 days of gestation, when the cervical neural epithelium has formed the neural tube and when the cephalic neural folds have elevated but not fused, were used. In addition, embryos in which the cephalic neural folds had been caused to re-open by culture in saline with low calcium were examined. Embryos were fixed and then fractured across the neural axis. A montage of the fractured edge of the neuroepithelium was prepared from a series of scanning electron micrographs. Cells of the neuroepithelium were classified according to the shapes of their profiles as rectangular, round, apically tapered, basally tapered or spindle-shaped, the last three categories being considered as 'tapered'. The outlines of the cells were digitised using a computer-linked graphics tablet to provide estimations of the perimeters (p) and areas (a) of the cell profiles, and the form factors, f. of the cell profiles were calculated by f = 4 pi a/p2. This factor is a unitless ratio which is unity for a circle and less than unity for any other shape. It provides a measure of the efficiency with which a perimeter encloses an area, and thus indicates the degree of deformation of a shape from circular. From 9.9 to 10.4 days the cervical neuroepithelium shows a decrease in the percentage of rectangular cells and an increase in the percentage of spindle-shaped cells. The mean form factors of cells in the apically tapered and spindle-shaped categories decrease, showing that these cells are more elongated and tapered in later embryos. When embryos at 10.4 days are cultured in saline with low calcium the elevated cephalic neural folds collapse. Concomitantly the percentage of round cells in the cephalic neural folds increases and the percentage of apically tapered and spindle-shaped cells decrease.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

Platelet size and shape in hereditary giant platelet syndromes on blood smear and in suspension: evidence for two types of abnormalities.

Platelet size on blood smear is compared with platelet size and shape in suspension (i.e., whole blood and citrated platelet-rich plasma [PRP]) for normal donors and 16 patients with hereditary "giant" platelet syndromes (HGPS), including Bernard-Soulier syndrome (BSS) (seven patients), Montreal platelet syndrome (MPS) (three patients), May-Hegglin anomaly (one patient) and Rafael platelet defect (one patient). In whole blood platelet shape is normal for HGPS, but in PRP for 10 of 16 patients with HGPS there is a decrease in the proportion of smooth, discoid-shaped platelets (discocytes [D]). The platelets of all patients with HGPS had abnormally large mean volume (VT) and increased size on peripheral blood smear. Furthermore, 12 of 16 patients with HGPS, including six of seven donors with BSS, had abnormally large discocytes. The measured size of HGPS shape-changed platelets was compared with the size predicted from the size of the D by assuming that the relationship between the size of shape-changed platelets and D was the same as observed for normal donors. In this manner it was shown that for all donors with BSS and MPS, the shape-changed platelets are disproportionately larger than the D. In contrast, in the remaining patients with HGPS the size of the shape-changed platelets was consistent with the size predicted from the D. Examination of VT for MPS as a function of time after addition of 10 mumol/L adenosine diphosphate to PRP revealed an abnormal time course, thereby pointing to an abnormality in the mechanisms that regulate platelet size during shape change. With the lone exceptions of BSS and MPS, the size of platelets on blood smear was well correlated with the total platelet plasma membrane surface area as measured by the osmotic spherocyte method. Our observations point to two distinct abnormalities in platelet size in HGPS: a disproportion between the size of D and "shape-changed" platelets, which may be related to an abnormal shape change and which is observed only for MPS and BSS, and an abnormal increase in platelet size on blood smear, which appears to reflect the increased amount of platelet plasma membrane in other HGPS platelets.

Adenosine Diphosphate↗