2,199 research outputs found

    Robust Non-Rigid Registration with Reweighted Position and Transformation Sparsity

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    Non-rigid registration is challenging because it is ill-posed with high degrees of freedom and is thus sensitive to noise and outliers. We propose a robust non-rigid registration method using reweighted sparsities on position and transformation to estimate the deformations between 3-D shapes. We formulate the energy function with position and transformation sparsity on both the data term and the smoothness term, and define the smoothness constraint using local rigidity. The double sparsity based non-rigid registration model is enhanced with a reweighting scheme, and solved by transferring the model into four alternately-optimized subproblems which have exact solutions and guaranteed convergence. Experimental results on both public datasets and real scanned datasets show that our method outperforms the state-of-the-art methods and is more robust to noise and outliers than conventional non-rigid registration methods.Comment: IEEE Transactions on Visualization and Computer Graphic

    AgriColMap: Aerial-Ground Collaborative 3D Mapping for Precision Farming

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    The combination of aerial survey capabilities of Unmanned Aerial Vehicles with targeted intervention abilities of agricultural Unmanned Ground Vehicles can significantly improve the effectiveness of robotic systems applied to precision agriculture. In this context, building and updating a common map of the field is an essential but challenging task. The maps built using robots of different types show differences in size, resolution and scale, the associated geolocation data may be inaccurate and biased, while the repetitiveness of both visual appearance and geometric structures found within agricultural contexts render classical map merging techniques ineffective. In this paper we propose AgriColMap, a novel map registration pipeline that leverages a grid-based multimodal environment representation which includes a vegetation index map and a Digital Surface Model. We cast the data association problem between maps built from UAVs and UGVs as a multimodal, large displacement dense optical flow estimation. The dominant, coherent flows, selected using a voting scheme, are used as point-to-point correspondences to infer a preliminary non-rigid alignment between the maps. A final refinement is then performed, by exploiting only meaningful parts of the registered maps. We evaluate our system using real world data for 3 fields with different crop species. The results show that our method outperforms several state of the art map registration and matching techniques by a large margin, and has a higher tolerance to large initial misalignments. We release an implementation of the proposed approach along with the acquired datasets with this paper.Comment: Published in IEEE Robotics and Automation Letters, 201

    Discontinuity preserving image registration for breathing induced sliding organ motion

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    Image registration is a powerful tool in medical image analysis and facilitates the clinical routine in several aspects. It became an indispensable device for many medical applications including image-guided therapy systems. The basic goal of image registration is to spatially align two images that show a similar region of interest. More speci�cally, a displacement �eld respectively a transformation is estimated, that relates the positions of the pixels or feature points in one image to the corresponding positions in the other one. The so gained alignment of the images assists the doctor in comparing and diagnosing them. There exist di�erent kinds of image registration methods, those which are capable to estimate a rigid transformation or more generally an a�ne transformation between the images and those which are able to capture a more complex motion by estimating a non-rigid transformation. There are many well established non-rigid registration methods, but those which are able to preserve discontinuities in the displacement �eld are rather rare. These discontinuities appear in particular at organ boundaries during the breathing induced organ motion. In this thesis, we make use of the idea to combine motion segmentation with registration to tackle the problem of preserving the discontinuities in the resulting displacement �eld. We introduce a binary function to represent the motion segmentation and the proposed discontinuity preserving non-rigid registration method is then formulated in a variational framework. Thus, an energy functional is de�ned and its minimisation with respect to the displacement �eld and the motion segmentation will lead to the desired result. In theory, one can prove that for the motion segmentation a global minimiser of the energy functional can be found, if the displacement �eld is given. The overall minimisation problem, however, is non-convex and a suitable optimisation strategy has to be considered. Furthermore, depending on whether we use the pure L1-norm or an approximation of it in the formulation of the energy functional, we use di�erent numerical methods to solve the minimisation problem. More speci�cally, when using an approximation of the L1-norm, the minimisation of the energy functional with respect to the displacement �eld is performed through Brox et al.'s �xed point iteration scheme, and the minimisation with respect to the motion segmentation with the dual algorithm of Chambolle. On the other hand, when we make use of the pure L1-norm in the energy functional, the primal-dual algorithm of Chambolle and Pock is used for both, the minimisation with respect to the displacement �eld and the motion segmentation. This approach is clearly faster compared to the one using the approximation of the L1-norm and also theoretically more appealing. Finally, to support the registration method during the minimisation process, we incorporate additionally in a later approach the information of certain landmark positions into the formulation of the energy functional, that makes use of the pure L1-norm. Similarly as before, the primal-dual algorithm of Chambolle and Pock is then used for both, the minimisation with respect to the displacement �eld and the motion segmentation. All the proposed non-rigid discontinuity preserving registration methods delivered promising results for experiments with synthetic images and real MR images of breathing induced liver motion

    Fiducial-Based Registration with Anisotropic Localization Error

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    Quantitative shape analysis with weighted covariance estimates for increased statistical efficiency

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    BACKGROUND: The introduction and statistical formalisation of landmark-based methods for analysing biological shape has made a major impact on comparative morphometric analyses. However, a satisfactory solution for including information from 2D/3D shapes represented by ‘semi-landmarks’ alongside well-defined landmarks into the analyses is still missing. Also, there has not been an integration of a statistical treatment of measurement error in the current approaches. RESULTS: We propose a procedure based upon the description of landmarks with measurement covariance, which extends statistical linear modelling processes to semi-landmarks for further analysis. Our formulation is based upon a self consistent approach to the construction of likelihood-based parameter estimation and includes corrections for parameter bias, induced by the degrees of freedom within the linear model. The method has been implemented and tested on measurements from 2D fly wing, 2D mouse mandible and 3D mouse skull data. We use these data to explore possible advantages and disadvantages over the use of standard Procrustes/PCA analysis via a combination of Monte-Carlo studies and quantitative statistical tests. In the process we show how appropriate weighting provides not only greater stability but also more efficient use of the available landmark data. The set of new landmarks generated in our procedure (‘ghost points’) can then be used in any further downstream statistical analysis. CONCLUSIONS: Our approach provides a consistent way of including different forms of landmarks into an analysis and reduces instabilities due to poorly defined points. Our results suggest that the method has the potential to be utilised for the analysis of 2D/3D data, and in particular, for the inclusion of information from surfaces represented by multiple landmark points

    Surface Reconstruction from Noisy and Sparse Data

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    We introduce a set of algorithms for registering, filtering and measuring the similarity of unorganized 3d point clouds, usually obtained from multiple views. We contribute a method for computing the similarity between point clouds that represent closed surfaces, specifically segmented tumors from CT scans. We obtain watertight surfaces and utilize volumetric overlap to determine similarity in a volumetric way. This similarity measure is used to quantify treatment variability based on target volume segmentation both prior to and following radiotherapy planning stages. We also contribute an algorithm for the drift-free registration of thin, non- rigid scans, where drift is the build-up of error caused by sequential pairwise registration, which is the alignment of each scan to its neighbor. We construct an average scan using mutual nearest neighbors, each scan is registered to this average scan, after which we update the average scan and continue this process until convergence. The use case herein is for merging scans of plants from multiple views and registering vascular scans together. Our final contribution is a method for filtering noisy point clouds, specif- ically those constructed from merged depth maps as obtained from a range scanner or multiple view stereo (MVS), applying techniques that have been utilized in finding outliers in clustered data, but not in MVS. We utilize ker- nel density estimation to obtain a probability density function over the space of observed points, utilizing variable bandwidths based on the nature of the neighboring points, Mahalanobis and reachability distances that is more dis- criminative than a classical Mahalanobis distance-based metric

    Gaussian Process Morphable Models

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    Statistical shape models (SSMs) represent a class of shapes as a normal distribution of point variations, whose parameters are estimated from example shapes. Principal component analysis (PCA) is applied to obtain a low-dimensional representation of the shape variation in terms of the leading principal components. In this paper, we propose a generalization of SSMs, called Gaussian Process Morphable Models (GPMMs). We model the shape variations with a Gaussian process, which we represent using the leading components of its Karhunen-Loeve expansion. To compute the expansion, we make use of an approximation scheme based on the Nystrom method. The resulting model can be seen as a continuous analogon of an SSM. However, while for SSMs the shape variation is restricted to the span of the example data, with GPMMs we can define the shape variation using any Gaussian process. For example, we can build shape models that correspond to classical spline models, and thus do not require any example data. Furthermore, Gaussian processes make it possible to combine different models. For example, an SSM can be extended with a spline model, to obtain a model that incorporates learned shape characteristics, but is flexible enough to explain shapes that cannot be represented by the SSM. We introduce a simple algorithm for fitting a GPMM to a surface or image. This results in a non-rigid registration approach, whose regularization properties are defined by a GPMM. We show how we can obtain different registration schemes,including methods for multi-scale, spatially-varying or hybrid registration, by constructing an appropriate GPMM. As our approach strictly separates modelling from the fitting process, this is all achieved without changes to the fitting algorithm. We show the applicability and versatility of GPMMs on a clinical use case, where the goal is the model-based segmentation of 3D forearm images

    Computed Tomography in the Modern Slaughterhouse

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    DoctorEye: A clinically driven multifunctional platform, for accurate processing of tumors in medical images

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    Copyright @ Skounakis et al.This paper presents a novel, open access interactive platform for 3D medical image analysis, simulation and visualization, focusing in oncology images. The platform was developed through constant interaction and feedback from expert clinicians integrating a thorough analysis of their requirements while having an ultimate goal of assisting in accurately delineating tumors. It allows clinicians not only to work with a large number of 3D tomographic datasets but also to efficiently annotate multiple regions of interest in the same session. Manual and semi-automatic segmentation techniques combined with integrated correction tools assist in the quick and refined delineation of tumors while different users can add different components related to oncology such as tumor growth and simulation algorithms for improving therapy planning. The platform has been tested by different users and over large number of heterogeneous tomographic datasets to ensure stability, usability, extensibility and robustness with promising results. AVAILABILITY: THE PLATFORM, A MANUAL AND TUTORIAL VIDEOS ARE AVAILABLE AT: http://biomodeling.ics.forth.gr. It is free to use under the GNU General Public License
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