nils-herrmann/clean_scirepeval huggingface dataset:
A modified fuzzy c-means algorithm for bias field estimation and segmentation of MRI data

We present a novel algorithm for fuzzy segmentation of magnetic resonance imaging (MRI) data and estimation of intensity inhomogeneities using fuzzy logic. MRI intensity inhomogeneities can be attributed to imperfections in the radio-frequency coils or to problems associated with the acquisition sequences. The result is a slowly varying shading artifact over the image that can produce errors with conventional intensity-based classification. Our algorithm is formulated by modifying the objective function of the standard fuzzy c-means (FCM) algorithm to compensate for such inhomogeneities and to allow the labeling of a pixel (voxel) to be influenced by the labels in its immediate neighborhood. The neighborhood effect acts as a regularizer and biases the solution toward piecewise-homogeneous labelings. Such a regularization is useful in segmenting scans corrupted by salt and pepper noise. Experimental results on both synthetic images and MR data are given to demonstrate the effectiveness and efficiency of the proposed algorithm.
Statistical morphable model for human teeth restoration

While traditional dental fillings are molded during a dental visit, dental restoration (e.g. inlays and onlays) are fabricated in a dental lab to offer a long lasting reparative solution to tooth decay or similar structural damage. Such process requires dental technicians who are highly trained experts in tooth anatomy to pick an appropriate standard tooth model from a tooth database. The success of a restoration process primarily relies on the acquisition and modeling of an accurate 3D shape of the occlusal surface of interest for manufacturing purposes. Based on a single optical image, this paper provides an economical and automated solution for tooth restoration where user intervention is kept at the minimal. The inherit relation between the photometric information and the underlying 3D shape is formulated as a coupled statistical model where the effect of illumination is modeled using Spherical Harmonics. Moreover, shape and texture alignment is accomplished using a proposed definition of anatomical jaw landmarks which are automatically detected. The system is evaluated on database of 32 jaws for crown, inlay, and onlay restoration. Results shows a promising performance for using the proposed approach in clinical application.
Distant face recognition based on sparse-stereo reconstruction

We introduce a framework for face recognition at a distance based on sparse-stereo reconstruction. We develop a 3D acquisition system that consists of two CCD stereo cameras mounted on pan-tilt units with adjustable baseline. We first detect the facial region and extract its landmark points, which are used to initialize an AAM mesh fitting algorithm. The fitted mesh vertices provide point correspondences between the left and right images of a stereo pair; stereo-based reconstruction is then used to infer the 3D information of the mesh vertices. We perform experiments regarding the use of different features extracted from these vertices for face recognition. The cumulative rank curves (CMC), which are generated using the proposed framework, confirms the feasibility of the proposed work for long distance recognition of human faces with respect to the state-of-the-art .
Robust centerline extraction framework using level sets

In this paper, we present a novel framework for computing centerlines for both 2D and 3D shape analysis. The framework works as follows: an object centerline point is selected automatically as the point of global maximum Euclidean distance from the boundary, and is considered a point source (Ps) that transmits a wave front that evolves over time and traverses the object domain. The front propagates at each object point with a speed that is proportional to its Euclidean distance from the boundary. The motion of the front is governed by a nonlinear partial differential equation whose solution is computed efficiently using level set methods. Initially, the P/sub S/ transmits a moderate speed wave to explore the object domain and extract its topological information such as merging and extreme points. Then, it transmits a new front that is much faster at centerline points than non central ones. As a consequence, centerlines intersect the propagating fronts at those points of maximum positive curvature. Centerlines are computed by tracking them, starting from each topological point until the Ps is reached, by solving an ordinary differential equation using an efficient numerical scheme. The proposed method is computationally inexpensive, handles efficiently objects with complex topology, and computes centerlines that are centered, connected, one point thick, and less sensitive to boundary noise. In addition, the extracted paths form a tree graph without additional cost. We have extensively validated the robustness of the proposed method both quantitatively and qualitatively against several 2D and 3D shapes.
One-sided transparency: A novel visualization for tubular objects

This paper describes a unique method for tubular object visualization. The method involves rendering the exterior of the tube invisible while keeping the interior visible. This “One-sided-transparency” technique renders a more complete view of the tube's interior. When applied to virtual colonoscopy (VC), it compares favorably to existing methods. It provides more complete images, reduces computational time, and reduces memory requirements while preserving VCs benefits for patients and practitioners. The approach also has various potential uses outside of VC.
Volume registration by surface point signature and mutual information maximization with applications in intra-operative MRI surgeries

Intra-operative MRI (iMRI) is a new technology that allows near real time updates of scans during a surgical procedure under the magnet. From an initial comprehensive scan, 3D volumes are obtained. During the surgery, only the portion of the organ under surgery needs to be re-scan (region of interest-ROI) in order to guide the progress of the surgery, and validate the procedure. We describe a registration approach which can be used for iMRI applications. Registration is performed through a hybrid of the surface point signature approach (SPS) and the maximization of the mutual information (MI) criterion. We demonstrate the approach on some real data.
Appearance-based approach for complete human jaw shape reconstruction

Precise knowledge of the 3D shape of clinical crowns is crucial for the treatment of malocclusion problems as well as several endodontic procedures. While computed tomography would present such information, it is believed there is no threshold radiation dose below which it is considered safe. In this study, the authors propose an appearance based approach which allows for the reconstruction of plausible human jaw 3D models given a single optical image with unknown illumination. Appearance bases are analytically constructed using the frequency-based representation of the irradiance equation while incorporating prior information about natural illumination and teeth reflectance. The inherent relation between the photometric information and the underlying 3D shape is formulated as a statistical model where the coupled effect of illumination and reflectance is modelled using the Helmholtz hemispherical harmonics-based irradiance harmonics whereas the principle component regression is deployed to carry out the estimation of 3D shapes. The authors' approach relaxes limiting assumptions of conventional shape-from-shading approaches while being able to reconstruct tooth occlusal surface with challenging conditions, such as scattered specular spots and significant changes in colour and albedo characteristics resulting from tooth filling. Vis-a-vis dental applications, the results demonstrate a significant increase in accuracy in favour of the proposed approach.
Heat front propagation contours for 3D face recognition

Face recognition is a key biometric method aiming at identifying individuals by the features of face. Due to the challenges facing face recognition from 2D images, researchers have resorted to 3D face recognition. Our work in this paper is motivated by the recent and remarkable success of heat-based features for 3D object classification and retrieval. We propose an approach for 3D face recognition based on the front contours of heat propagation over the face surface. The front contours are extracted automatically as heat is propagating starting from a detected set of landmarks. The propagation contours are used to successfully discriminate the various faces. The proposed approach is evaluated on the largest publicly available database of 3D facial images and successfully compared to the state-of-the-art approaches in the literature.
New Approach for Classification of Autistic vs. Typically Developing Brain Using White Matter Volumes

Autism is a complex developmental disability, characterized by deficits in social interaction, communication skills, range of interests, and occasionally the presence of stereotyped behaviors. Several studies show that changes in brain weight and volume over aging follow a unique trajectory in those affected by the condition~\cite{MICCAIMost00}. In this work, we develop a robust technique for evaluating the volume of white matter (WM), and use it as the main classification criteria. We perform MRI-based analysis on the brains of 14 autistic and 28 control subjects, male and female between aged 7 to 38 years. The proposed framework consists of several stages. First, the entire T1-weighted MRI scans are filtered out from noise using anisotropic diffusion filter. Then, the white matter (WM) is segmented from the skull. The segmentation framework is the search for maximum-a-posterior configurations in a Markov Gibbs Random Field (MGRF) model. A 3D mesh is then generated from the segmented WM. Finally, the volume of the 3D mesh is computed using a new algorithm. The experiments show accurate classification results of the proposed framework.
Object recognition using neural networks and surface signatures

We present a concept for 3D free-form object recognition using a surface representation scheme. This representation scheme captures the 3D curvature information of any free-form surface and encodes it into a 2D image corresponding to a certain point on the surface. This image is unique for this point and is independent from the object translation or orientation in space. For this reason we called this image the surface point signature (SPS). Using specially designed neural networks; the SPS images are used in the matching and recognition of 3D objects in a 3D scanned scene.
Two-stage neural network for volume segmentation of medical images

We present a system to segment and label CT/MRI brain slices using feature extraction and unsupervised clustering. In this technique, each voxel is assigned a feature pattern consisting of a scaled family of differential geometrical invariant features. The invariant feature pattern is then assigned to a specific region using a two-stage neural network system. The first stage is a self-organizing principal components analysis (SOPCA) network that is used to project the feature vector onto its leading principal axes found by using principal components analysis. This step provides an effective basis for feature extraction. The second stage consists of a self-organizing feature map (SOFM) which will automatically cluster the input vector into different regions. The optimum number of regions (clusters) is obtained by a model fitting approach. Finally, a 3D connected component labeling algorithm is applied to ensure region connectivity. Implementation and performance of this technique are presented. Compared to other approaches, the new system is more accurate in extracting 3D anatomical structures of the brain, and can be adapted to real-time imaging scenarios.
A new segmentation and registration approach for vertebral body analysis

To diagnose the osteoporosis accurately, the bone mineral density (BMD) measurements of the vertebral bodies (VBs) are required. In this paper, we propose a new segmentation and registration method in order to assist the BMD measurements and fracture analysis (FA) accurately. In this experiment, image appearance and shape information of VBs are used. Our shape model is required to be registered to the testing image to avoid user interaction(s). Our proposed framework has four phases: i) the detection of vertebral body (VB) using the Matched filter, ii) initial segmentation using the intensity and spatial interaction models, iii) the registration of the shape prior and initially segmented image by matching a vector distance function (VDF), and iv) final segmentation using graph cuts which integrates intensity, spatial interaction and shape prior. Preliminary results show that our new algorithm is very promising and can solve many segmentation and registration problems.
Thermal Imaging of the Superficial Temporal Artery: An Arterial Pulse Recovery Model

We present a novel model for measurement of the arterial pulse from the superficial temporal artery (STA) using passive thermal infrared (IR) sensors. The proposed approach has a physical and physiological basis and as such is of fundamental nature. Thermal IR camera is used to capture the heat pattern from superficial arteries, and a blood vessel model is used to describe the pulsatile nature of the blood flow. A multiresolution wavelet-based signal analysis approach is used to extract the arterial pulse waveform, which lends itself to various physiological measurements. We validate the results using a traditional contact vital-sign monitor as a ground truth. Eight people of different age, race and gender have been tested in our study consistent with IRB approval. The resultant arterial pulse waveforms exactly matched the ground-truth readings. The essence of our approach is the automatic detection of region of arterial pulse measurement (ROM), from which the arterial pulse waveform is extracted. To the best of our knowledge, the correspondence between non-contact thermal IR imaging based measurements of the arterial pulse in the time domain and traditional contact approaches has never been reported in the literature.
A probabilistic framework for combining tracking algorithms

For the past few years researches have been investigating enhancing tracking performance by combining several different tracking algorithms. We propose an analytically justified, probabilistic framework to combine multiple tracking algorithms. The separate tracking algorithms considered output a probability distribution function of the tracked state, sequentially for each image. The algorithms may output either an explicit probability distribution function, or a sample-set of it via condensation. The proposed framework is general and allows the combination of any set of separate tracking algorithms of this kind, even on different state spaces of different dimensionality, under a few reasonable assumptions. In many of the investigated settings, our approach allows us to treat the separate tracking algorithms as "closed boxes ". In other words, only the state distributions in the input and output are needed for the combination process. The suggested framework was successfully tested using various state spaces and datasets.
Virtual Forces for Camera Planning in Smart Vision Systems

In this paper, we present a novel and robust approach for camera planning in smart vision systems. The proposed approach uses virtual forces to adjust the camera parameters (pan, tilt, translation ... etc.) toward the most proper values with respect to the application. It employs the physical spring model to direct the motion of the camera toward its target. Our approach is a general framework and any vision system can be easily modeled to use it. This approach has several advantages over previous work in camera planning. It is portable, expandable, robust, and flexible. We present a case study of a two degree-of-freedom stereo vision system to test our approach. The results show the efficiency of our approach even with poor system initialization and its robustness against possible weakness in the auxiliary algorithms used.
Free-form surface registration using surface signatures

The paper introduces a new free-form surface representation scheme for the purpose of fast and accurate registration and matching. Accurate registration of surfaces is a common task in computer vision. The proposed representation scheme captures the surface curvature information seen from certain points and produces images called surface signatures at these points. Matching signatures of different surfaces enables the recovery of the transformation parameters between these surfaces. We propose to use template matching to compare the signature images. To enable partial matching, another criterion, the overlap ratio, is used. This representation scheme can be used as a global representation of the surface as well as a local one and performs near real time registration. We show that the signature representation can be used to match objects in 3D scenes in the presence of clutter and occlusion. Applications presented include free-form object matching, multimodal medical volume registration and dental teeth reconstruction from intra-oral images.
Geometric Features Based Framework for Colonic Polyp Detection using a New Color Coding Scheme

Curvature-based geometric features have been proven to be important for colonic polyp detection. In this paper, we present an automatic detection framework and color coding scheme to highlight the detected polyps. The key idea is to place the detected polyps at the same locations in a newly created polygonal dataset with the same topology and geometry properties as the triangulated mesh surface of real colon dataset, and assign different colors to the two separated datasets to highlight the polyps. Finally, we validate the proposed framework by computer simulated and real colon datasets. For fifteen synthetic polyps with different shapes and different sizes, the sensitivity is 100%, and false positive is 0. For four real colon datasets, the proposed algorithm has achieved the sensitivity of 75%.
Facial expression recognition based on geometric and optical flow features in colour image sequences

Facial expression recognition is a useful feature in modern human computer interaction (HCI). In order to build efficient and reliable recognition systems, face detection, feature extraction and classification have to be robustly realised. Addressing the latter two issues, this work proposes a new method based on geometric and transient optical flow features and illustrates their comparison and integration for facial expression recognition. In the authors' method, photogrammetric techniques are used to extract three-dimensional (3-D) features from every image frame, which is regarded as a geometric feature vector. Additionally, optical flow-based motion detection is carried out between consecutive images, what leads to the transient features. Artificial neural network and support vector machine classification results demonstrate the high performance of the proposed method. In particular, through the use of 3-D normalisation and colour information, the proposed method achieves an advanced feature representation for the accurate and robust classification of facial expressions.
A two-step fuzzy-Bayesian classification for high dimensional data

The goal of this paper is twofold. First, we present a supervised fuzzy c-mean (SFCM) classifier for the classification of high dimensional data. Comparisons of the conventional FCM clustering technique and Bayesian classification technique are also presented. Next, we present a two-step classifier in which the proposed SFCM and Bayesian algorithms are used in a cooperative way such that classification results of the SFCM algorithm are used to compute the prior probabilities required for the Bayesian classifier. Classification results of the three algorithms are presented on simulated and real remote sensing multispectral data. The results obtained show improvements in the classification accuracy and reliability using the two-step algorithm.
MAP region segmentation based on composite random field models

A composite of two random field models is used to describe the observed image: a high-level process that describes the various regions in the images is modeled by a Gibbs-Markov model, and a low-level process that describes each particular region is modeled by a simultaneous autoregressive model. Using this composition, a recursive maximum a posterior (MAP) segmentation algorithm is formulated and various issues related to parameter estimation are discussed.<<ETX>>
Statistical modeling of the lung nodules in low dose computed tomography scans of the chest

This work presents a novel approach in automatic detection of the lung nodules and is compared with respect to parametric nodule models in terms of sensitivity and specificity. A Statistical method is used for generating data driven models of the nodules appearing in low dose CT (LDCT) scans of the human chest. Four types of common lung nodules are analyzed using the Procrustes based AAM method to create descriptive lung nodules. Performance of the new nodule models on clinical datasets is significant over parametric nodule models in both sensitivity and specificity. The new nodule modeling approach is also applicable for automatic classification of nodules into pathologies given a descriptive database. This approach is a major step forward for early diagnosis of lung cancer.
Variational-based method to extract parametric shapes from images

In this paper, we propose a variational method to segment image objects, which have a given parametric shape based on a level-set formulation of the Mumford-Shah functional, and the shape parameters. We define an energy functional composed by two complementary terms. The first one detects object boundaries using a Chan-Vese-like method. The second term constrains the contour to find a shape compatible with the parametric shape. The segmentation of the object of interest is given by the minimum of our energy functional. This minimum is computed with the calculus of variation and the gradient descent method that provide a system of evolution equations solved with the well-known level set method. We focus in this paper on the parametric category of image linear objects. Applications of the proposed model are presented on synthetic and real images
Deformable models for random small-size objects: Case of lung nodules in CT tomography

Deformable models are common in image modeling and analysis. Random objects provide major challenges as shapes and appearances are hard to quantify; hence, formulation of deformable models are much harder to construct and validate. In this paper, we examine the effect of randomness on building the shape and appearance models for small-size lung nodules (≤ 1cm) which appear in computed tomography (CT) of the human chest. We devise an approach for annotation, which lends a standard mechanism for building traditional active appearance (AAM), active shape (ASM) and active tensor models (ATM). We illustrate the effectiveness of AAM for nodule detection.