Affine Iterative Closest Point Algorithm Based on Color Information and Correntropy for Precise Point Set Registration.

In this paper, we propose a novel affine iterative closest point algorithm based on color information and correntropy, which can effectively deal with the registration problems with a large number of noise and outliers and small deformations in RGB-D datasets. Firstly, to alleviate the problem of low registration accuracy for data with weak geometric structures, we consider introducing color features into traditional affine algorithms to establish more accurate and reliable correspondences. Secondly, we introduce the correntropy measurement to overcome the influence of a large amount of noise and outliers in the RGB-D datasets, thereby further improving the registration accuracy. Experimental results demonstrate that the proposed registration algorithm has higher registration accuracy, with error reduction of almost 10 times, and achieves more stable robustness than other advanced algorithms.

Efficient Similarity Point Set Registration by Transformation Decomposition.

Point set registration is one of the basic problems in computer vision. When the overlap ratio between point sets is small or the relative transformation is large, local methods cannot guarantee the accuracy. However, the time complexity of the branch and bound (BnB) optimization used in most existing global methods is exponential in the dimensionality of parameter space. Therefore, seven-Degrees of Freedom (7-DoF) similarity transformation is a big challenge for BnB. In this paper, a novel rotation and scale invariant feature is introduced to decouple the optimization of translation, rotation, and scale in similarity point set registration, so that BnB optimization can be done in two lower dimensional spaces. With the transformation decomposition, the translation is first estimated and then the rotation is optimized by maximizing a robust objective function defined on consensus set. Finally, the scale is estimated according to the potential correspondences in the obtained consensus set. Experiments on synthetic data and clinical data show that our method is approximately two orders of magnitude faster than the state-of-the-art global method and more accurate than a typical local method. When the outlier ratio with respect to the inliers is up to 1.0, our method still achieves accurate registration.

A Robust Nonrigid Point Set Registration Method Based on Collaborative Correspondences.

The nonrigid point set registration is one of the bottlenecks and has the wide applications in computer vision, pattern recognition, image fusion, video processing, and so on. In a nonrigid point set registration problem, finding the point-to-point correspondences is challengeable because of the various image degradations. In this paper, a robust method is proposed to accurately determine the correspondences by fusing the two complementary structural features, including the spatial location of a point and the local structure around it. The former is used to define the absolute distance (AD), and the latter is exploited to define the relative distance (RD). The AD-correspondences and the RD-correspondences can be established based on AD and RD, respectively. The neighboring corresponding consistency is employed to assign the confidence for each RD-correspondence. The proposed heuristic method combines the AD-correspondences and the RD-correspondences to determine the corresponding relationship between two point sets, which can significantly improve the corresponding accuracy. Subsequently, the thin plate spline (TPS) is employed as the transformation function. At each step, the closed-form solutions of the affine and nonaffine parts of TPS can be independently and robustly solved. It facilitates to analyze and control the registration process. Experimental results demonstrate that our method can achieve better performance than several existing state-of-the-art methods.

A Review of Point Set Registration: From Pairwise Registration to Groupwise Registration.

This paper presents a comprehensive literature review on point set registration. The state-of-the-art modeling methods and algorithms for point set registration are discussed and summarized. Special attention is paid to methods for pairwise registration and groupwise registration. Some of the most prominent representative methods are selected to conduct qualitative and quantitative experiments. From the experiments we have conducted on 2D and 3D data, CPD-GL pairwise registration algorithm and JRMPC groupwise registration algorithm seem to outperform their rivals both in accuracy and computational complexity. Furthermore, future research directions and avenues in the area are identified.

A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.

Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction.

Articulated Non-Rigid Point Set Registration for Human Pose Estimation from 3D Sensors.

We propose a generative framework for 3D human pose estimation that is able to operate on both individual point sets and sequential depth data. We formulate human pose estimation as a point set registration problem, where we propose three new approaches to address several major technical challenges in this research. First, we integrate two registration techniques that have a complementary nature to cope with non-rigid and articulated deformations of the human body under a variety of poses. This unique combination allows us to handle point sets of complex body motion and large pose variation without any initial conditions, as required by most existing approaches. Second, we introduce an efficient pose tracking strategy to deal with sequential depth data, where the major challenge is the incomplete data due to self-occlusions and view changes. We introduce a visible point extraction method to initialize a new template for the current frame from the previous frame, which effectively reduces the ambiguity and uncertainty during registration. Third, to support robust and stable pose tracking, we develop a segment volume validation technique to detect tracking failures and to re-initialize pose registration if needed. The experimental results on both benchmark 3D laser scan and depth datasets demonstrate the effectiveness of the proposed framework when compared with state-of-the-art algorithms.

Applying Machine Learning and Point-Set Registration to Automatically Measure the Severity of Spinal Curvature on Radiographs.

OBJECTIVE: Measuring the severity of the lateral spinal curvature, or Cobb angle, is critical for monitoring and making treatment decisions for children with adolescent idiopathic scoliosis (AIS). However, manual measurement is time-consuming and subject to human error. Therefore, clinicians seek an automated measurement method to streamline workflow and improve accuracy. This paper reports on a novel machine learning algorithm of cascaded convolutional neural networks (CNN) to measure the Cobb angle on spinal radiographs automatically. METHODS: The developed method consisted of spinal column segmentation using a CNN, vertebra localization and segmentation using iterative vertebra body location coupled with another CNN, point-set registration to correct vertebra segmentations, and Cobb angle measurement using the final segmentations. Measurement performance was evaluated with the circular mean absolute error (CMAE) and percentage within clinical acceptance ([Formula: see text]) between automatic and manual measurements. Analysis was separated by curve severity to identify any potential systematic biases using independent samples Student's t-tests. RESULTS: The method detected 346 of the 352 manually measured Cobb angles (98%), with a CMAE of 2.8° and 91% of measurements within the 5° clinical acceptance. No statistically significant differences were found between the CMAEs of mild ([Formula: see text]), moderate (25°-45°), and severe ([Formula: see text]) groups. The average measurement time per radiograph was 17.7±10.2s, improving upon the estimated average of 30s it takes an experienced rater to measure. Additionally, the algorithm outputs segmentations with the measurement, allowing clinicians to interpret measurement results. DISCUSSION/CONCLUSION: The developed method measured Cobb angles on radiographs automatically with high accuracy, quick measurement time, and interpretability, suggesting clinical feasibility.

Multi-constraint point set registration with redundant point removal for the registration of coronary arteries.

BACKGROUND: Coronary artery disease (CAD) is the leading cause of death worldwide. The registration of the coronary artery at different phases can help radiologists explore the motion patterns of the coronary artery and assist in the diagnosis of CAD. However, there is no automatic and easy-to-execute method to solve the missing data problem that occurs at the endpoints of the coronary artery tree. This paper proposed a non-rigid multi-constraint point set registration with redundant point removal (MPSR-RPR) algorithm to tackle this challenge. METHODS: Firstly, the MPSR-RPR algorithm roughly registered two coronary artery point sets with the pre-set smoothness regularization parameter and Gaussian filter width value. The moving coherent, local feature, and the corresponding relationship between bifurcation point pairs were exploited as the constraints. Next, the spatial geometry information of the coronary artery was utilized to automatically recognize the vessel endpoints and to delete the redundant points of the coronary artery. Finally, the algorithm continued carrying out the multi-constraint registration with another group of the pre-set parameters to improve the alignment performance. RESULTS: The experimental results demonstrated that the MPSR-RPR algorithm achieved a significantly lower mean value of the modified Hausdorff distance (MHD) compared to the other state-of-the-art methods for addressing the serious missing data in the left and right coronary arteries. CONCLUSION: This study demonstrated the effectiveness of the proposed algorithm in aligning coronary arteries, providing significant value in assisting in the diagnosis of coronary artery and myocardial lesions.

Estimation of coronary artery movement using a non-rigid registration with global-local structure preservation.

BACKGROUND: At present, coronary artery disease (CAD) is the leading cause of death worldwide. Many studies have shown that CAD is strongly associated with the motion characteristics of the coronary arteries. Although cardiovascular imaging technology has been widely used for the diagnosis of CAD, the motion parameters of the heart and coronary arteries cannot be directly calculated from the images. In this paper, we propose a point set registration method with global and local topology constraints to quantify coronary artery movement. METHODS: The global constraint is the motion coherence of the point set which enforces the smoothness of the displacement field. The local linear embedding based topological structure and the local feature descriptor i.e., the 3D shape context, are designed to retain the local structure of the point set. We incorporate these constraints into a maximum likelihood framework and derive an expectation-maximization algorithm to obtain the transformation function between the two point sets. The proposed method was compared with four existing algorithms using simulated data and applied to the real data obtained from 4D CT angiograms. RESULTS: For the simulation data, the proposed method achieves a lower registration error than the comparison algorithms. For the real data, the proposed method shows that, in most cases, the right coronary artery achieves a larger velocity than the left anterior descending and left circumflex branches, and there are three well-defined velocity peaks, during the cardiac cycle for these branches. CONCLUSION: The proposed approach is feasible and effective in quantifying coronary artery movement and thus adds to the diagnostic power of coronary imaging.

Global optimization point-set registration based on translation/rotation decoupling for image-guided surgery applications.

PURPOSE: In image-guided surgery systems, image-to-patient spatial registration is to get the spatial transformation between the image space and the actual operating space. Although the image-to-patient spatial registration methods using paired point or surface matching are used in some image-guided neurosurgery systems, the key problem is that the global optimization registration result cannot be achieved. Therefore, this paper proposes a new rotation invariant feature for decoupling rotation and translation space, based on which global optimization point set registration method is proposed. METHODS: The new rotation invariant features, constructed based on the edges and the angles, are the rotation invariant, which has high feature resolution. Some of them are not only the rotation invariant, but also the translation invariant. To obtain the global optimal solution, branch and bound search strategy is used to search the parameter space of the translation and the computational cost is reduced simultaneously. The registration accuracy of the spatial registration method is analyzed by comparing the difference between the estimated transform and the standard transform to calculate the registration error. RESULTS: To validate the performance of the spatial registration method proposed, the registration performance was analyzed by comparing the experimental results with the results of the two mainstream registration methods (the iterative closest point [ICP] registration method and the coherent point drift method). In the experiments, the comparison was based on the registration accuracy and the execution time. We show our registration method can obtain higher accuracy in a shorter time in most cases. At the same time, when using ICP to further refine our results, the ICP method can converge in a very short time, which also shows that our method provides a good initial pose for the ICP method and can help the ICP converge to the global optimal solution faster. Our method can achieve an average rotation error of 0.124 degrees and an average translation error of 0.38 mm on 10 clinical data. CONCLUSIONS: The results reveal that the surface registration method based on translation rotation decoupling can achieve superior performance regarding both the registration accuracy and the time efficiency in the image-to-patient spatial registration.

Real-time multimodal image registration with partial intraoperative point-set data.

We present Free Point Transformer (FPT) - a deep neural network architecture for non-rigid point-set registration. Consisting of two modules, a global feature extraction module and a point transformation module, FPT does not assume explicit constraints based on point vicinity, thereby overcoming a common requirement of previous learning-based point-set registration methods. FPT is designed to accept unordered and unstructured point-sets with a variable number of points and uses a "model-free" approach without heuristic constraints. Training FPT is flexible and involves minimizing an intuitive unsupervised loss function, but supervised, semi-supervised, and partially- or weakly-supervised training are also supported. This flexibility makes FPT amenable to multimodal image registration problems where the ground-truth deformations are difficult or impossible to measure. In this paper, we demonstrate the application of FPT to non-rigid registration of prostate magnetic resonance (MR) imaging and sparsely-sampled transrectal ultrasound (TRUS) images. The registration errors were 4.71 mm and 4.81 mm for complete TRUS imaging and sparsely-sampled TRUS imaging, respectively. The results indicate superior accuracy to the alternative rigid and non-rigid registration algorithms tested and substantially lower computation time. The rapid inference possible with FPT makes it particularly suitable for applications where real-time registration is beneficial.

A random-sampling approach to track cell divisions in time-lapse fluorescence microscopy.

BACKGROUND: Particle-tracking in 3D is an indispensable computational tool to extract critical information on dynamical processes from raw time-lapse imaging. This is particularly true with in vivo time-lapse fluorescence imaging in cell and developmental biology, where complex dynamics are observed at high temporal resolution. Common tracking algorithms used with time-lapse data in fluorescence microscopy typically assume a continuous signal where background, recognisable keypoints and independently moving objects of interest are permanently visible. Under these conditions, simple registration and identity management algorithms can track the objects of interest over time. In contrast, here we consider the case of transient signals and objects whose movements are constrained within a tissue, where standard algorithms fail to provide robust tracking. RESULTS: To optimize 3D tracking in these conditions, we propose the merging of registration and tracking tasks into a registration algorithm that uses random sampling to solve the identity management problem. We describe the design and application of such an algorithm, illustrated in the domain of plant biology, and make it available as an open-source software implementation. The algorithm is tested on mitotic events in 4D data-sets obtained with light-sheet fluorescence microscopy on growing Arabidopsis thaliana roots expressing CYCB::GFP. We validate the method by comparing the algorithm performance against both surrogate data and manual tracking. CONCLUSION: This method fills a gap in existing tracking techniques, following mitotic events in challenging data-sets using transient fluorescent markers in unregistered images.

An open-source tool for the validation of finite element models using three-dimensional full-field measurements.

Three-dimensional (3D) full-field measurements provide a comprehensive and accurate validation of finite element (FE) models. For the validation, the result of the model and measurements are compared based on two respective point-sets and this requires the point-sets to be registered in one coordinate system. Point-set registration is a non-convex optimization problem that has widely been solved by the ordinary iterative closest point algorithm. However, this approach necessitates a good initialization without which it easily returns a local optimum, i.e. an erroneous registration. The globally optimal iterative closest point (Go-ICP) algorithm has overcome this drawback and forms the basis for the presented open-source tool that can be used for the validation of FE models using 3D full-field measurements. The capability of the tool is demonstrated using an application example from the field of biomechanics. Methodological problems that arise in real-world data and the respective implemented solution approaches are discussed.

Technical Note: A comparison of point set registration methods for electromagnetic tracking.

PURPOSE: High dose rate brachytherapy applies intense and destructive radiation. A treatment plan defines radiation source dwell positions to avoid irradiating healthy tissue. The study discusses methods to quantify any positional changes of source locations along the various treatment sessions. METHODS: Electromagnetic tracking (EMT) localizes the radiation source during the treatment sessions. But in each session the relative position of the patient relative to the filed generator is changed. Hence, the measured dwell point sets need to be registered onto each other to render them comparable. Two point set registration techniques are compared: a probabilistic method called coherent point drift (CPD) and a multidimensional scaling (MDS) technique. RESULTS: Both enable using EMT without external registration and achieve very similar results with respect to dwell position determination of the radiation source. Still MDS achieves smaller grand average deviations (CPD-rPSR: MD = 2.55 mm, MDS-PSR: MD = 2.15 mm) between subsequent dwell position determinations, which also show less variance (CPD-rPSR: IQR = 4 mm, MDS-PSR: IQR = 3 mm). Furthermore, MDS is not based on approximations and does not need an iterative procedure to track sensor positions inside the implanted catheters. CONCLUSION: Although both methods achieve similar results, MDS is to be preferred over rigid CPD while nonrigid CPD is unsuitable as it does not preserve topology.

Coupled Morphological-Hemodynamic Computational Analysis of Type B Aortic Dissection: A Longitudinal Study.

Progressive false lumen aneurysmal degeneration in type B aortic dissection (TBAD) is a complex process with a multi-factorial etiology. Patient-specific computational fluid dynamics (CFD) simulations provide spatial and temporal hemodynamic quantities that facilitate understanding this disease progression. A longitudinal study was performed for a TBAD patient, who was diagnosed with the uncomplicated TBAD in 2006 and treated with optimal medical therapy but received surgery in 2010 due to late complication. Geometries of the aorta in 2006 and 2010 were reconstructed. With registration algorithms, we accurately quantified the evolution of the false lumen, while with CFD simulations we computed several hemodynamic indexes, including the wall shear stress (WSS), and the relative residence time (RRT). The numerical fluid model included large eddy simulation (LES) modeling for efficiently capturing the flow disturbances induced by the entry tears. In the absence of complete patient-specific data, the boundary conditions were based on a specific calibration method. Correlations between hemodynamics and the evolution field in time obtained by registration of the false lumen are discussed. Further testing of this methodology on a large cohort of patients may enable the use of CFD to predict whether patients, with originally uncomplicated TBAD, develop late complications.

Group-wise similarity registration of point sets using Student's t-mixture model for statistical shape models.

A probabilistic group-wise similarity registration technique based on Student's t-mixture model (TMM) and a multi-resolution extension of the same (mr-TMM) are proposed in this study, to robustly align shapes and establish valid correspondences, for the purpose of training statistical shape models (SSMs). Shape analysis across large cohorts requires automatic generation of the requisite training sets. Automated segmentation and landmarking of medical images often result in shapes with varying proportions of outliers and consequently require a robust method of alignment and correspondence estimation. Both TMM and mrTMM are validated by comparison with state-of-the-art registration algorithms based on Gaussian mixture models (GMMs), using both synthetic and clinical data. Four clinical data sets are used for validation: (a) 2D femoral heads (K= 1000 samples generated from DXA images of healthy subjects); (b) control-hippocampi (K= 50 samples generated from T1-weighted magnetic resonance (MR) images of healthy subjects); (c) MCI-hippocampi (K= 28 samples generated from MR images of patients diagnosed with mild cognitive impairment); and (d) heart shapes comprising left and right ventricular endocardium and epicardium (K= 30 samples generated from short-axis MR images of: 10 healthy subjects, 10 patients diagnosed with pulmonary hypertension and 10 diagnosed with hypertrophic cardiomyopathy). The proposed methods significantly outperformed the state-of-the-art in terms of registration accuracy in the experiments involving synthetic data, with mrTMM offering significant improvement over TMM. With the clinical data, both methods performed comparably to the state-of-the-art for the hippocampi and heart data sets, which contained few outliers. They outperformed the state-of-the-art for the femur data set, containing large proportions of outliers, in terms of alignment accuracy, and the quality of SSMs trained, quantified in terms of generalization, compactness and specificity.

Automatic Sulcal Curve Extraction with MRF Based Shape Prior.

Extracting and labeling sulcal curves on the human cerebral cortex is important for many neuroscience studies, however manually annotating the sulcal curves is a time-consuming task. In this paper, we present an automatic sulcal curve extraction method by registering a set of dense landmark points representing the sulcal curves to the subject cortical surface. A Markov random field is used to model the prior distribution of these landmark points, with short edges in the graph preserving the curve structure and long edges modeling the global context of the curves. Our approach is validated using a leave-one-out strategy of training and evaluation on fifteen cortical surfaces, and a quantitative error analysis on the extracted major sulcal curves.

Simultaneous Cortical Surface Labeling and Sulcal Curve Extraction.

Automatic labeling of the gyri and sulci on the cortical surface is important for studying cortical morphology and brain functions within populations. A method to simultaneously label gyral regions and extract sulcal curves is proposed. Assuming that the gyral regions parcellate the whole cortical surface into contiguous regions with certain fixed topology, the proposed method labels the subject cortical surface by deformably registering a network of curves that form the boundary of gyral regions to the subject cortical surface. In the registration process, the curves are encouraged to follow the fine details of the sulcal geometry and to observe the shape statistics learned from training data. Using the framework of probabilistic point set registration methods, the proposed algorithm finds the sulcal curve network that maximizes the posterior probability by Expectation-Maximization (EM). The automatic labeling method was evaluated on 15 cortical surfaces using a leave-one-out strategy. Quantitative error analysis is carried out on both labeled regions and major sulcal curves.