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  • 1. Auer, M.
    et al.
    Gasser, T. Christian
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.).
    Reconstruction and Finite Element Mesh Generation of Abdominal Aortic Aneurysms From Computerized Tomography Angiography Data With Minimal User Interactions2010In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 29, no 4, 1022-1028 p.Article in journal (Refereed)
    Abstract [en]

    Evaluating rupture risk of abdominal aortic aneurysms is critically important in reducing related mortality without unnecessarily increasing the rate of elective repair. According to the current clinical practice aneurysm rupture risk is (mainly) estimated from its maximum diameter and/or expansion rate; an approach motivated from statistics but known to fail often in individuals. In contrast, recent research demonstrated that patient specific biomechanical simulations can provide more reliable diagnostic parameters, however current structural model development is cumbersome and time consuming. This paper used 2D and 3D deformable models to reconstruct aneurysms from computerized tomography angiography data with minimal user interactions. In particular, formulations of frames and shells, as known from structural mechanics, were used to define deformable modes, which in turn allowed a direct mechanical interpretation of the applied set of reconstruction parameters. Likewise, a parallel finite element implementation of the models allows the segmentation of clinical cases on standard personal computers within a few minutes. The particular topology of the applied 3D deformable models supports a fast and simple hexahedral-dominated meshing of the arising generally polyhedral domain. The variability of the derived segmentations (luminal: 0.50(SD 0.19) mm; exterior 0.89(SD 0.45) mm) with respect to large variations in elastic properties of the deformable models was in the range of the differences between manual segmentations as performed by experts (luminal: 0.57(SD 0.24) mm; exterior: 0.77(SD 0.58) mm), and was particularly independent from the algorithm's initialization. The proposed interaction of deformable models and mesh generation defines finite element meshes suitable to perform accurate and efficient structural analysis of the aneurysm using mixed finite element formulations.

  • 2. Auer, M.
    et al.
    Stollberger, R.
    Regitnig, P.
    Ebner, F.
    Holzapfel, Gerhard A.
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.), Biomechanics.
    3-D reconstruction of tissue components for atherosclerotic human arteries using ex vivo high-resolution MRI2006In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 25, no 3, 345-357 p.Article in journal (Refereed)
    Abstract [en]

    Automatic computer-based methods are well suited for the image analysis of the different components in atherosclerotic plaques. Although several groups work on such analysis some of the methods used are oversimplified and require improvements when used within a computational framework for predicting meaningful stress and strain distributions in the heterogeneous arterial wall under various loading conditions. Based on high-resolution magnetic resonance imaging of excised atherosclerotic human arteries and a series of two-dimensional (2-D) contours we present a segmentation tool that permits a three-dimensional (3-D) reconstruction of the most important tissue components of atherosclerotic arteries. The underlying principle of the proposed approach is a model-based snake algorithm for identifying 2-D contours, which uses information about the plaque composition and geometric data of the tissue layers. Validation of the computer-generated tissue boundaries is performed with 100 MR images, which are compared with the results of a manual segmentation performed by four experts. Based on the Hausdorff distance and the average distance for computer-to-expert differences and the interexpert differences for the outer boundary of the adventitia, the adventitia-media, media-intima, intima-lumen and calcification boundaries are less than 1 pixel (0.234 mm). The percentage statistic shows similar results to the modified Williams index in terms of accuracy. Except for the identification of lipid-rich regions the proposed algorithm is automatic. The nonuniform rational B-spline-based computer-generated 3-D models of the individual tissue components provide a basis for clinical and computational analysis.

  • 3. Bernard, Olivier
    et al.
    Bosch, J G
    Heyde, Brecht
    Alessandrini, Martino
    Barbosa, Daniel
    Camarasu-Pop, S
    Cervenansky, F
    Valette, S
    Mirea, O
    Bernier, M
    Jodoin, P M
    Domingos, J S
    Stebbing, R V
    Keraudren, K
    Oktay, O
    Caballero, J
    Shi, W
    Rueckert, D
    Milletari, F
    Ahmadi, S A
    Smistad, E
    Lindseth, F
    van Stralen, M
    Wang, Chunliang
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Image Processing and Visualization.
    Smedby, Örjan
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Image Processing and Visualization.
    Donal, E
    Monaghan, M
    Papachristidis, A
    Geleijnse, M L
    Galli, E
    Dhooge, Jan
    Standardized evaluation system for left ventricular segmentation algorithms in 3D echocardiography.2015In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254XArticle in journal (Refereed)
    Abstract [en]

    Real-time 3D Echocardiography (RT3DE) has been proven to be an accurate tool for left ventricular (LV) volume assessment. However, identification of the LV endocardium remains a challenging task, mainly because of the low tissue/blood contrast of the images combined with typical artifacts. Several semi and fully automatic algorithms have been proposed for segmenting the endocardium in RT3DE data in order to extract relevant clinical indices, but a systematic and fair comparison between such methods has so far been impossible due to the lack of a publicly available common database. Here, we introduce a standardized evaluation framework to reliably evaluate and compare the performance of the algorithms developed to segment the LV border in RT3DE. A database consisting of 45 multivendor cardiac ultrasound recordings acquired at different centers with corresponding reference measurements from 3 experts are made available. The algorithms from nine research groups were quantitatively evaluated and compared using the proposed online platform. The results showed that the best methods produce promising results with respect to the experts' measurements for the extraction of clinical indices, and that they offer good segmentation precision in terms of mean distance error in the context of the experts' variability range. The platform remains open for new submissions.

  • 4.
    Bornefalk, Hans
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Physics of Medical Imaging.
    Persson, Mats
    KTH, School of Engineering Sciences (SCI), Physics, Physics of Medical Imaging.
    Theoretical Comparison of the Iodine Quantification Accuracy of Two Spectral CT Technologies2014In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 33, no 2, 556-565 p.Article in journal (Refereed)
    Abstract [en]

    We compare the theoretical limits of iodine quantification for the photon counting multibin and dual energy technologies. Dual energy systems by necessity have to make prior assumptions in order to quantify iodine. We explicitly allow the multibin system to make the same assumptions and also allow them to be wrong. We isolate the effect of technology from imperfections and implementation issues by assuming both technologies to be ideal, i.e., without scattered radiation, unity detection efficiency and perfect energy response functions, and by applying the Cramer-Rao lower bound methodology to assess the quantification accuracy. When priors are wrong the maximum likelihood estimates will be biased and the mean square error of the quantification error is a more appropriate figure of merit. The evaluation assumes identical X-ray spectra for both methodologies and for that reason a sensitivity analysis is performed with regard to the assumed X-ray spectrum. We show that when iodine is quantified over regions of interest larger than 6 cm, multibin systems benefit by independent estimation of three basis functions. For smaller regions of interest multibin systems can increase quantification accuracy by making the same prior assumptions as dual energy systems.

  • 5.
    Bornefalk, Hans
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Physics of Medical Imaging.
    Persson, Mats
    KTH, School of Engineering Sciences (SCI), Physics, Physics of Medical Imaging.
    Danielsson, Mats
    KTH, School of Engineering Sciences (SCI), Physics, Physics of Medical Imaging.
    Allowable forward model misspecification for accurate basis decomposition in a silicon detector based spectral CT2015In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 34, no 3, 788-795 p.Article in journal (Refereed)
    Abstract [en]

    Material basis decomposition in the sinogram domain requires accurate knowledge of the forward model in spectral computed tomography (CT). Misspecifications over a certain limit will result in biased estimates and make quantum limited (where statistical noise dominates) quantitative CT difficult. We present a method whereby users can determine the degree of allowed misspecification error in a spectral CT forward model and still have quantification errors that are limited by the inherent statistical uncertainty. For a particular silicon detector based spectral CT system, we conclude that threshold determination is the most critical factor and that the bin edges need to be known to within 0.15 keV in order to be able to perform quantum limited material basis decomposition. The method as such is general to all multibin systems.

  • 6. Gopinath, A.
    et al.
    Xu, G.
    Ress, D.
    Öktem, Ozan
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.). KTH, School of Engineering Sciences (SCI), Centres, Center for Industrial and Applied Mathematics, CIAM.
    Subramaniam, S.
    Bajaj, C.
    Shape-based regularization of electron tomographic reconstruction2012In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 31, no 12, 2241-2252 p.Article in journal (Refereed)
    Abstract [en]

    We introduce a tomographic reconstruction method implemented using a shape-based regularization technique. Spatial models of known features in the structure being reconstructed are integrated into the reconstruction process as regularizers. Our regularization scheme is driven locally through shape information obtained from segmentation and compared with a known spatial model. We demonstrated our method on tomography data from digital phantoms, simulated data, and experimental electron tomography (ET) data of virus complexes. Our reconstruction showed reduced blurring and an improvement in the resolution of the reconstructed volume was also measured. This method also produced improved demarcation of spike boundaries in viral membranes when compared with popular techniques like weighted back projection and the algebraic reconstruction technique. Improved ET reconstructions will provide better structure elucidation and improved feature visualization, which can aid in solving key biological issues. Our method can also be generalized to other tomographic modalities.

  • 7. Jimenez-del-Toro, Oscar
    et al.
    Muller, Henning
    Krenn, Markus
    Gruenberg, Katharina
    Taha, Abdel Aziz
    Winterstein, Marianne
    Eggel, Ivan
    Foncubierta-Rodriguez, Antonio
    Goksel, Orcun
    Jakab, Andres
    Kontokotsios, Georgios
    Langs, Georg
    Menze, Bjoern H.
    Fernandez, Tomas Salas
    Schaer, Roger
    Walleyo, Anna
    Weber, Marc-Andre
    Cid, Yashin Dicente
    Gass, Tobias
    Heinrich, Mattias
    Jia, Fucang
    Kahl, Fredrik
    Kechichian, Razmig
    Mai, Dominic
    Spanier, Assaf B.
    Vincent, Graham
    Wang, Chunliang
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Image Processing and Visualization.
    Wyeth, Daniel
    Hanbury, Allan
    Cloud-Based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms: VISCERAL Anatomy Benchmarks2016In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 35, no 11, 2459-2475 p.Article in journal (Refereed)
    Abstract [en]

    Variations in the shape and appearance of anatomical structures in medical images are often relevant radiological signs of disease. Automatic tools can help automate parts of this manual process. A cloud-based evaluation framework is presented in this paper including results of benchmarking current state-of-the-art medical imaging algorithms for anatomical structure segmentation and landmark detection: the VISCERAL Anatomy benchmarks. The algorithms are implemented in virtual machines in the cloud where participants can only access the training data and can be run privately by the benchmark administrators to objectively compare their performance in an unseen common test set. Overall, 120 computed tomography and magnetic resonance patient volumes were manually annotated to create a standard Gold Corpus containing a total of 1295 structures and 1760 landmarks. Ten participants contributed with automatic algorithms for the organ segmentation task, and three for the landmark localization task. Different algorithms obtained the best scores in the four available imaging modalities and for subsets of anatomical structures. The annotation framework, resulting data set, evaluation setup, results and performance analysis from the three VISCERAL Anatomy benchmarks are presented in this article. Both the VISCERAL data set and Silver Corpus generated with the fusion of the participant algorithms on a larger set of non-manually-annotated medical images are available to the research community.

  • 8.
    Larsson, David
    et al.
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging. KTH.
    Spühler, Jeannette Hiromi
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Petersson, Sven
    Karolinska Universitetssjukhuset.
    Nordenfur, Tim
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging.
    Colarieti-Tosti, Massimiliano
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging.
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Winter, Reidar
    Karolinska Institutet.
    Larsson, Matilda
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging.
    Patient-Specific Left Ventricular Flow Simulations From Transthoracic Echocardiography: Robustness Evaluation and Validation Against Ultrasound Doppler and Magnetic Resonance Imaging2017In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 36, no 11, 2261-2275 p.Article in journal (Refereed)
    Abstract [en]

    The combination of medical imaging with computational fluid dynamics (CFD) has enabled the study of 3D blood flow on a patient-specificlevel. However, with models based on gated high-resolution data, the study of transient flows, and any model implementation into routine cardiac care, is challenging. The present paper presents a novel pathway for patient-specific CFD modelling of the left ventricle (LV), using 4D transthoracic echocardiography (TTE) as input modality. To evaluate the clinical usability, two sub-studies were performed. First, a robustness evaluation was performed where repeated models with alternating input variables were generated for 6 subjects and changes in simulated output quantified. Second, a validation study was carried out where the pathway accuracy was evaluated against pulsed-wave Doppler (100 subjects), and 2D through-plane phase-contrast magnetic resonance imaging measurements over 7 intraventricular planes (6 subjects). The robustness evaluation indicated a model deviation of <12%, with highest regional and temporal deviations at apical segments and at peak systole, respectively. The validation study showed an error of < 11% (velocities < 10 cm/s) for all subjects, with no significant regional or temporal differences observed. With the patient-specific pathway shown to provide robust output with high accuracy, and with the pathway dependent only on 4DTTE, the method has a high potential to be used within future clinical studies on 3D intraventricular flowpatterns. To this, future model developments in the form of e.g. anatomically accurate LV valves may further enhance the clinical value of the simulations.

  • 9. Lilledahl, Magnus B.
    et al.
    Pierce, David M.
    Ricken, Tim
    Holzapfel, Gerhard A.
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.), Biomechanics.
    Davies, Catharina de Lange
    Structural Analysis of Articular Cartilage Using Multiphoton Microscopy: Input for Biomechanical Modeling2011In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 30, no 9, 1635-1648 p.Article in journal (Refereed)
    Abstract [en]

    The 3-D morphology of chicken articular cartilage was quantified using multiphoton microscopy (MPM) for use in continuum-mechanical modeling. To motivate this morphological study we propose aspects of a new, 3-D finite strain constitutive model for articular cartilage focusing on the essential load-bearing morphology: an inhomogeneous, poro-(visco) elastic solid matrix reinforced by an anisotropic, (visco) elastic dispersed fiber fabric which is saturated by an incompressible fluid residing in strain-dependent pores. Samples of fresh chicken cartilage were sectioned in three orthogonal planes and imaged using MPM, specifically imaging the collagen fibers using second harmonic generation. Employing image analysis techniques based on Fourier analysis, we derived the principal directionality and dispersion of the collagen fiber fabric in the superficial layer. In the middle layer, objective thresholding techniques were used to extract the volume fraction occupied by extracellular collagen matrix. In conjunction with information available in the literature, or additional experimental testing, we show how this data can be used to derive a 3-D map of the initial solid volume fraction and Darcy permeability.

  • 10.
    Magnusson, Klas E. G.
    et al.
    KTH, School of Electrical Engineering (EES), Signal Processing.
    Jaldén, Joakim
    KTH, School of Electrical Engineering (EES), Signal Processing.
    Gilbert, Penney M.
    Blau, Helen M.
    Global linking of cell tracks using the Viterbi algorithm2015In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 34, no 4, 911-929 p.Article in journal (Refereed)
    Abstract [en]

    Automated tracking of living cells in microscopy image sequences is an important and challenging problem. With this application in mind, we propose a global track linking algorithm, which links cell outlines generated by a segmentation algorithm into tracks. The algorithm adds tracks to the image sequence one at a time, in a way which uses information from the complete image sequence in every linking decision. This is achieved by finding the tracks which give the largest possible increases to a probabilistically motivated scoring function, using the Viterbi algorithm. We also present a novel way to alter previously created tracks when new tracks are created, thus mitigating the effects of error propagation. The algorithm can handle mitosis, apoptosis, and migration in and out of the imaged area, and can also deal with false positives, missed detections, and clusters of jointly segmented cells. The algorithm performance is demonstrated on two challenging datasets acquired using bright-field microscopy, but in principle, the algorithm can be used with any cell type and any imaging technique, presuming there is a suitable segmentation algorithm.

  • 11.
    Nillius, Peter
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Medical Imaging.
    Danielsson, Mats
    KTH, School of Engineering Sciences (SCI), Physics, Medical Imaging.
    Theoretical Bounds and System Design for Multipinhole SPECT2010In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 29, no 7, 1390-1400 p.Article in journal (Refereed)
    Abstract [en]

    The pinhole camera in single photon emission computed tomography (SPECT) has an inherent trade-off between resolution and sensitivity. Recent systems overcome this to some extent by utilizing multiple pinholes distributed around the imaging object. The present work is a theoretical study on how to optimally construct such systems. We use an analytic model to analyze the multipinhole SPECT geometry and identify the underlying trade-offs. One of the results is the derivation of the upper bound for the sensitivity, given the geometric resolution and field-of-view (FOV). Reaching this bound requires an infinitely large detector. However, a sensitivity very close to the upper bound can be achieved by a system with realistic proportions. We show that it is usually possible to get a sensitivity that is 95%-99% of the upper bound. Further analysis reveals a trade-off between sensitivity, magnification, and the number of pinholes. Based on this new theory, we develop a strategy for multipinhole SPECT design, from which a number of example systems are computed. Penetration in the pinhole knife edge is accounted for by using the resolution and sensitivity equivalent apertures.

  • 12.
    Persson, Mats
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Medical Imaging.
    Bornefalk, Hans
    KTH, School of Engineering Sciences (SCI), Physics, Medical Imaging.
    A Framework for Evaluating Threshold Variation Compensation Methods in Photon Counting Spectral CT2012In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 31, no 10, 1861-1874 p.Article in journal (Refereed)
    Abstract [en]

    One of the challenges in the development of photon counting spectral computed tomography (CT) detectors is that the location of the energy thresholds tends to vary among detector elements. If not compensated for, this threshold variation leads to ring artifacts in the reconstructed images. In this paper, a framework is presented for the systematic comparison of different methods of compensating for inhomogeneities among detector elements in photon counting CT with multiple energy bins. Furthermore, we propose the use of an affine minimum mean square error estimator, calibrated against transmission measurements on different combinations of two materials, for inhomogeneity compensation. Using the framework developed here, this method is compared to two other compensation schemes, flatfielding using an air scan and signal-to-thickness calibration using a step wedge calibrator, in a simulation study. The results show that for all but the lowest studied level of threshold spread, the proposed method is superior to signal-to-thickness calibration, which in turn is superior to flatfielding. We also demonstrate that the effects of threshold variation can be countered to a large extent by substructuring each detector element into depth segments.

  • 13.
    Yveborg, Moa
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Physics of Medical Imaging.
    Danielsson, Mats
    KTH, School of Engineering Sciences (SCI), Physics, Physics of Medical Imaging.
    Bornefalk, Hans
    KTH, School of Engineering Sciences (SCI), Physics, Physics of Medical Imaging.
    Theoretical comparison of a dual energy system and photon counting silicon detector used for material quantification in spectral CT2015In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 34, no 3, 796-806 p.Article in journal (Refereed)
    Abstract [en]

    Any method using dual energy computed tomography (CT) has to make prior assumptions in order to quantify k-edge contrast agents. This work estimates the mean square error (MSE) in contrast agent quantification employing a method based on assigning each reconstructed voxel a ratio of soft tissue and fat using dual energy CT. The results are compared to the MSE using a photon counting silicon detector with multiple bins. The square root of the MSEs of the quantifications of iodine and gadolinium for an object consisting of soft tissue and fat using the silicon detector and dual energy CT range from below 2% and 1% of the contrast agent content for 100 ${rm mg}/{rm cm}^{3}$ of iodine and gadolinium, up to approximately 10% and 13%, and 6% and 4%, for 5 ${rm mg}/{rm cm}^{3}$ of iodine and gadolinium, respectively. When adding bone with a voxel volume fraction of 2.2%, the square root of the MSEs of the quantifications of iodine and gadolinium using dual energy CT increases to 25% and 6%, respectively, for 5 ${rm mg}/{rm cm}^{3}$ of contrast agent. In conclusion, results indicate that the noise levels of the material quantification using the silicon detector are higher than the noise levels using a dual energy CT when the composition of the object is known. However, using a dual energy CT increases the risk of model specification error and subsequently a large bias in contrast agent quantification, a problem which does not exist when using a multi-bin CT where the number of energy bins is larger than two.

  • 14.
    Yveborg, Moa
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Physics of Medical Imaging.
    Hans, Bornefalk
    KTH, School of Engineering Sciences (SCI), Physics, Physics of Medical Imaging.
    Mats, Persson
    KTH, School of Engineering Sciences (SCI), Physics, Physics of Medical Imaging.
    Optimal frequency-based weighting for spectral x-ray projection imaging2015In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 34, no 3, 779-787 p.Article in journal (Refereed)
    Abstract [en]

    The purpose of this work is to derive a weighting scheme that maximizes the frequency-dependent ideal observer signal-difference-to-noise ratio, commonly referred to as detectability index or Hotelling-SDNR, for spectral X-ray projection imaging. Starting from basic statistical decision theory, optimal frequency-dependent weights are derived for a multiple-bin system and the Hotelling-SDNR calculated. A 28% increase in detectability index is found for high frequency objects when applying optimal frequency-dependent weights instead of pixel-based weights to a simplified model of a silicon detector, decreasing towards 0% for low frequency objects. Simulation results indicate a potentially large increase in detectability for high-frequency object imaging using silicon detectors, thus meriting further evaluations on a real system.

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