nils-herrmann/clean_scirepeval huggingface dataset:
Robust ultrasound image analysis using learning

Robust and accurate analysis of clinical ultrasound data is a challenging task due to the complexity of scanned anatomy, noise, shadows, signal dropouts and quantity of the information to be processed. As a result, traditional image analysis relying on the explicit encoding of prior knowledge such as perceptual grouping, variational or generative approaches is usually not enough to capture the complex appearance of ultrasound data. We will discuss a new class of methods that build on recent advances in discriminative machine learning to achieve robust and efficient performance. Image analysis is formulated as a multi-scale learning problem through which object models of increasing complexity are progressively learned. We will demonstrate example applications in Cardiology and OB/GYN.
Simultaneous Registration and Modeling of Deformable Shapes

Many natural objects vary the shapes as linear combinations of certain bases. The measurement of such deformable shapes is coupling of rigid similarity transformations between the objects and the measuring systems and non-rigid deformations controlled by the linear bases. Thus registration and modeling of deformable shapes are coupled problems, where registration is to compute the rigid transformations and modeling is to construct the linear bases. The previous methods [3, 2] separate the solution into two steps. The first step registers the measurements regarding the shapes as rigid and the deformations as random noise. The second step constructs the linear model using the registered shapes. Since the deformable shapes do not vary randomly but are constrained by the underlying model, such separate steps result in registration biased by nonrigid deformations and shape models involving improper rigid transformations. We for the first time present this bias problem and formulate that, the coupled registration and modeling problems are essentially a single factorization problem and thus require a simultaneous solution. We then propose the Direct Factorization method that extends a structure from motion method . It yields a linear closedform solution that simultaneously registers the deformable shapes at arbitrary dimensions (2D \to 2D, 3D \to 3D, . . .) and constructs the linear bases. The accuracy and robustness of the proposed approach are demonstrated quantitatively on synthetic data and qualitatively on real shapes.
Efficient Lattice Boltzmann Solver for Patient-Specific Radiofrequency Ablation of Hepatic Tumors

Radiofrequency ablation (RFA) is an established treatment for liver cancer when resection is not possible. Yet, its optimal delivery is challenged by the presence of large blood vessels and the time-varying thermal conductivity of biological tissue. Incomplete treatment and an increased risk of recurrence are therefore common. A tool that would enable the accurate planning of RFA is hence necessary. This manuscript describes a new method to compute the extent of ablation required based on the Lattice Boltzmann Method (LBM) and patient-specific, pre-operative images. A detailed anatomical model of the liver is obtained from volumetric images. Then a computational model of heat diffusion, cellular necrosis, and blood flow through the vessels and liver is employed to compute the extent of ablated tissue given the probe location, ablation duration and biological parameters. The model was verified against an analytical solution, showing good fidelity. We also evaluated the predictive power of the proposed framework on ten patients who underwent RFA, for whom pre- and post-operative images were available. Comparisons between the computed ablation extent and ground truth, as observed in postoperative images, were promising (DICE index: 42%, sensitivity: 67%, positive predictive value: 38%). The importance of considering liver perfusion while simulating electrical-heating ablation was also highlighted. Implemented on graphics processing units (GPU), our method simulates 1 minute of ablation in 1.14 minutes, allowing near real-time computation.
Learning-based hypothesis fusion for robust catheter tracking in 2D X-ray fluoroscopy

Catheter tracking has become more and more important in recent interventional applications. It provides real time navigation for the physicians and can be used to control a motion compensated fluoro overlay reference image for other means of guidance, e.g. involving a 3D anatomical model. Tracking the coronary sinus (CS) catheter is effective to compensate respiratory and cardiac motion for 3D overlay navigation to assist positioning the ablation catheter in Atrial Fibrillation (Afib) treatments. During interventions, the CS catheter performs rapid motion and non-rigid deformation due to the beating heart and respiration. In this paper, we model the CS catheter as a set of electrodes. Novelly designed hypotheses generated by a number of learning-based detectors are fused. Robust hypothesis matching through a Bayesian framework is then used to select the best hypothesis for each frame. As a result, our tracking method achieves very high robustness against challenging scenarios such as low SNR, occlusion, foreshortening, non-rigid deformation, as well as the catheter moving in and out of ROI. Quantitative evaluation has been conducted on a database of 13221 frames from 1073 sequences. Our approach obtains 0.50mm median error and 0.76mm mean error. 97.8% of evaluated data have errors less than 2.00mm. The speed of our tracking algorithm reaches 5 frames-per-second on most data sets. Our approach is not limited to the catheters inside the CS but can be extended to track other types of catheters, such as ablation catheters or circumferential mapping catheters.
Accurate polyp segmentation for 3D CT colongraphy using multi-staged probabilistic binary learning and compositional model

Accurate and automatic colonic polyp segmentation and measurement in Computed Tomography (CT) has significant importance for 3D polyp detection, classification, and more generally computer aided diagnosis of colon cancers. In this paper, we propose a three-staged probabilistic binary classification approach for automatically segmenting polyp voxels from their surrounding tissues in CT. Our system integrates low-, and mid-level information for discriminative learning under local polar coordinates which align on the 3D colon surface around detected polyp. More importantly, our supervised learning system has flexible modeling capacity, which offers a principled means of encoding semantic, clinical expert annotations of colonic polyp tissue identification and segmentation. The learning generality to unseen data is bounded by boosting [12, 11] and stacked generality . Extensive experimental results on polyp segmentation performance evaluation and robustness testing with disturbances (using both training data and unseen data) are provided to validate our presented approach. The reliability of polyp segmentation and measurement has been largely increased to 98:2% (ie. errors les 3 mm), compared with other state of art work [4, 15] of about 75% ~ 80%.
Image-Based Multiclass Boosting and Echocardiographic View Classification

We tackle the problem of automatically classifying cardiac view for an echocardiographic sequence as a multiclass object detection. As a solution, we present an imagebased multiclass boosting procedure. In contrast with conventional approaches for multiple object detection that train multiple binary classifiers, one per object, we learn only one multiclass classifier using the LogitBoosting algorithm. To utilize the fact that, in the midst of boosting, one class is fully separated from the remaining classes, we propose to learn a tree structure that focuses on the remaining classes to improve learning efficiency. Further, we accommodate the large number of background images using a cascade of boosted multiclass classifiers, which is able to simultaneously detect and classify multiple objects while rejecting the background class quickly. Our experiments on echocardiographic view classification demonstrate promising performances of image-based multiclass boosting.
Automatic Detection and Measurement of Structures in Fetal Head Ultrasound Volumes Using Sequential Estimation and Integrated Detection Network (IDN)

Routine ultrasound exam in the second and third trimesters of pregnancy involves manually measuring fetal head and brain structures in 2-D scans. The procedure requires a sonographer to find the standardized visualization planes with a probe and manually place measurement calipers on the structures of interest. The process is tedious, time consuming, and introduces user variability into the measurements. This paper proposes an automatic fetal head and brain (AFHB) system for automatically measuring anatomical structures from 3-D ultrasound volumes. The system searches the 3-D volume in a hierarchy of resolutions and by focusing on regions that are likely to be the measured anatomy. The output is a standardized visualization of the plane with correct orientation and centering as well as the biometric measurement of the anatomy. The system is based on a novel framework for detecting multiple structures in 3-D volumes. Since a joint model is difficult to obtain in most practical situations, the structures are detected in a sequence, one-by-one. The detection relies on Sequential Estimation techniques, frequently applied to visual tracking. The interdependence of structure poses and strong prior information embedded in our domain yields faster and more accurate results than detecting the objects individually. The posterior distribution of the structure pose is approximated at each step by sequential Monte Carlo. The samples are propagated within the sequence across multiple structures and hierarchical levels. The probabilistic model helps solve many challenges present in the ultrasound images of the fetus such as speckle noise, signal drop-out, shadows caused by bones, and appearance variations caused by the differences in the fetus gestational age. This is possible by discriminative learning on an extensive database of scans comprising more than two thousand volumes and more than thirteen thousand annotations. The average difference between ground truth and automatic measurements is below 2 mm with a running time of 6.9 s (GPU) or 14.7 s (CPU). The accuracy of the AFHB system is within inter-user variability and the running time is fast, which meets the requirements for clinical use.
A learning based hierarchical model for vessel segmentation

In this paper we present a learning based method for vessel segmentation in angiographic videos. Vessel segmentation is an important task in medical imaging and has been investigated extensively in the past. Traditional approaches often require pre-processing steps, standard conditions or manually set seed points. Our method is automatic, fast and robust towards noise often seen in low radiation X-ray images. Furthermore, it can be easily trained and used for any kind of tubular structure. We formulate the segmentation task as a hierarchical learning problem over 3 levels: border points, cross-segments and vessel pieces, corresponding to the vessel's position, width and length. Following the marginal space learning paradigm the detection on each level is performed by a learned classifier. We use probabilistic boosting trees with Haar and steerable features. First results of segmenting the vessel which surrounds a guide wire in 200 frames are presented and future additions are discussed.
Automatic Cardiac View Classification of Echocardiogram

We propose a fully automatic system for cardiac view classification of echocardiogram. Given an echo study video sequence, the system outputs a view label among the pre-defined standard views. The system is built based on a machine learning approach that extracts knowledge from an annotated database. It characterizes three features: 1) integrating local and global evidence, 2) utilizing view specific knowledge, and 3) employing a multi-class Logit-boost algorithm. In our prototype system, we classify four standard cardiac views: apical four chamber and apical two chamber, parasternal long axis and parasternal short axis (at mid cavity). We achieve a classification accuracy over 96% both of training and test data sets and the system runs in a second in the environment of Pentium 4 PC with 3.4 GHz CPU and 1.5 G RAM.
Automatic Detection and Segmentation of Lymph Nodes From CT Data

Lymph nodes are assessed routinely in clinical practice and their size is followed throughout radiation or chemotherapy to monitor the effectiveness of cancer treatment. This paper presents a robust learning-based method for automatic detection and segmentation of solid lymph nodes from CT data, with the following contributions. First, it presents a learning based approach to solid lymph node detection that relies on marginal space learning to achieve great speedup with virtually no loss in accuracy. Second, it presents a computationally efficient segmentation method for solid lymph nodes (LN). Third, it introduces two new sets of features that are effective for LN detection, one that self-aligns to high gradients and another set obtained from the segmentation result. The method is evaluated for axillary LN detection on 131 volumes containing 371 LN, yielding a 83.0% detection rate with 1.0 false positive per volume. It is further evaluated for pelvic and abdominal LN detection on 54 volumes containing 569 LN, yielding a 80.0% detection rate with 3.2 false positives per volume. The running time is 5-20 s per volume for axillary areas and 15-40 s for pelvic. An added benefit of the method is the capability to detect and segment conglomerated lymph nodes.
A Probabilistic Model for Automatic Segmentation of the Esophagus in 3-D CT Scans

Being able to segment the esophagus without user interaction from 3-D CT data is of high value to radiologists during oncological examinations of the mediastinum. The segmentation can serve as a guideline and prevent confusion with pathological tissue. However, limited contrast to surrounding structures and versatile shape and appearance make segmentation a challenging problem. This paper presents a multistep method. First, a detector that is trained to learn a discriminative model of the appearance is combined with an explicit model of the distribution of respiratory and esophageal air. In the next step, prior shape knowledge is incorporated using a Markov chain model. We follow a “detect and connect” approach to obtain the maximum a posteriori estimate of the approximate esophagus shape from hypothesis about the esophagus contour in axial image slices. Finally, the surface of this approximation is nonrigidly deformed to better fit the boundary of the organ. The method is compared to an alternative approach that uses a particle filter instead of a Markov chain to infer the approximate esophagus shape, to the performance of a human observer and also to state of the art methods, which are all semiautomatic. Cross-validation on 144 CT scans showed that the Markov chain based approach clearly outperforms the particle filter. It segments the esophagus with a mean error of 1.80 mm in less than 16 s on a standard PC. This is only 1 mm above the interobserver variability and can compete with the results of previously published semiautomatic methods.
Advanced intervention planning for Transcatheter Aortic Valve Implantations (TAVI) from CT using volumetric models

Aortic valve stenosis is a serious heart disease affecting a large group of elderly people. Recently minimal invasive procedures, such as the Transcatheter Aortic Valve Implantation (TAVI), are beginning to substitute conventional surgical techniques. Current methods  can extract basic biomarkers for TAVI such as optimal C-arm angulations, area and diameter measurements. However as the most prevalent TAVI complications (stroke and paravalvular leakages) are correlated with calcium and leaflet interactions within the valve a more advanced solution is needed. We propose a fully integrated system to extract automatically the patient specific model of the aortic valve including the volumetric model of the aortic valve leaflets and calcium from high resolution single phase CT. Based on the volumetric model advanced clinical parameters can be derived and used for e.g. patient selection, paravalvular leakage prediction and patient stroke risk assessment. We employ robust machine learning algorithms to estimate the valve model parameters. A multi-class classification method is introduced to label regions of calcium, leaflet and blood pool within the aortic valve and extract volumetric models of the aortic valve leaflets. Extensive quantitative and qualitative experiments on 198 volumetric data sets demonstrate an accurate DICE similarity score, i.e. 0.7 for the aortic valve leaflets and 0.86 for calcium tissue. Within 6 seconds a complete patient-specific model of the aortic valve can be estimated.
Search strategies for multiple landmark detection by submodular maximization

A fundamental issue in multiple landmark detection is the reduction of computational cost. This problem has previously been addressed mainly by reducing the complexity of each individual landmark detector. We address the problem by optimizing the search strategy of multiple landmarks. When the relative positions of landmarks are constrained, the search space can be reduced, thereby reducing the computation. The proposed method leverages the theory of submodular functions to provide a constant factor approximation guarantee of the optimal speed. Although the theory of submodular functions is well known, to the best of our knowledge, this is the first time it is applied to the landmark detection problem. We demonstrate our method by fast and accurate detection of human body landmarks including bones, organs, and vessels in 3D CT images from a diverse dataset of around 2000 volumes with pathological patients. We further provide different search space criteria and variations.
3D ultrasound tracking of the left ventricle using one-step forward prediction and data fusion of collaborative trackers

Tracking the left ventricle (LV) in 3D ultrasound data is a challenging task because of the poor image quality and speed requirements. Many previous algorithms applied standard 2D tracking methods to tackle the 3D problem. However, the performance is limited due to increased data size, landmarks ambiguity, signal drop-out or non-rigid deformation. In this paper we present a robust, fast and accurate 3D LV tracking algorithm. We propose a novel one-step forward prediction to generate the motion prior using motion manifold learning, and introduce two collaborative trackers to achieve both temporal consistency and failure recovery. Compared with tracking by detection and 3D optical flow, our algorithm provides the best results and sub-voxel accuracy. The new tracking algorithm is completely automatic and computationally efficient. It requires less than 1.5 seconds to process a 3D volume which contains 4,925,440 voxels.
Retrieval performance improvement through low rank corrections

Whenever a feature extracted from an image has a unimodal distribution, information about its covariance matrix can be exploited for content based retrieval using as dissimilarity measure, the Bhattacharyya distance. To reduce the amount of computations and the size of logical database entry, we approximate the Bhattacharyya distance, taking into account that most of the energy in the feature space is often restricted to a low dimensional subspace. The theory was tested for a database of 1188 textures derived from VisTex with the local texture being represented by a 15 dimensional MRSAR feature vector. The retrieval performance improved significantly, relative to the traditional Mahalanobis distance based approach, in spite of using only one or two dimensions in the approximation.
Robust guidewire tracking in fluoroscopy

A guidewire is a medical device inserted into vessels during image guided interventions for balloon inflation. During interventions, the guidewire undergoes non-rigid deformation due to patients' breathing and cardiac motions, and such 3D motions are complicated when being projected onto the 2D fluoroscopy. Furthermore, in fluoroscopy there exist severe image artifacts and other wire-like structures. All these make robust guidewire tracking challenging. To address these challenges, this paper presents a probabilistic framework for robust guidewire tracking. We first introduce a semantic guidewire model that contains three parts, including a catheter tip, a guidewire tip and a guidewire body. Measurements of different parts are integrated into a Bayesian framework as measurements of a whole guidewire for robust guidewire tracking. Moreover, for each part, two types of measurements, one from learning-based detectors and the other from online appearance models, are applied and combined. A hierarchical and multi-resolution tracking scheme is then developed based on kernel-based measurement smoothing to track guidewires effectively and efficiently in a coarse-to-fine manner. The presented framework has been validated on a test set of 47 sequences, and achieves a mean tracking error of less than 2 pixels. This demonstrates the great potential of our method for clinical applications.
Robust object detection using marginal space learning and ranking-based multi-detector aggregation: Application to left ventricle detection in 2D MRI images

Magnetic resonance imaging (MRI) is currently the gold standard for left ventricle (LV) quantification. Detection of the LV in an MRI image is a prerequisite for functional measurement. However, due to the large variations in the orientation, size, shape, and image intensity of the LV, automatic LV detection is challenging. In this paper, we propose to use marginal space learning (MSL) to exploit the recent advances in learning discriminative classifiers. Unlike full space learning (FSL) where a monolithic classifier is trained directly in the five dimensional object pose space (two for position, one for rotation, and two for anisotropic scaling), we train three detectors, namely, the position detector, the position-orientation detector, and the position-orientation-scale detector. As a contribution of this paper, we perform thorough comparison between MSL and FSL. Experiments show MSL significantly outperforms FSL on both the training and test sets. Additionally, we also detect several LV landmarks, such as the LV apex and two annulus points. If we combine the detected candidates from both the whole-object detector and landmark detectors, we can further improve the system robustness even when one detector fails. A novel ranking-based strategy is proposed to combine the detected candidates from all detectors. Experiments show our ranking-based aggregation approach can significantly reduce the detection outliers.
The variable bandwidth mean shift and data-driven scale selection

We present two solutions for the scale selection problem in computer vision. The first one is completely nonparametric and is based on the the adaptive estimation of the normalized density gradient. Employing the sample point estimator, we define the Variable Bandwidth Mean Shift, prove its convergence, and show its superiority over the fixed bandwidth procedure. The second technique has a semiparametric nature and imposes a local structure on the data to extract reliable scale information. The local scale of the underlying density is taken as the bandwidth which maximizes the magnitude of the normalized mean shift vector. Both estimators provide practical tools for autonomous image and quasi real-time video analysis and several examples are shown to illustrate their effectiveness.