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Li, Z. (author), Van Vliet, L.J. (author), Stoker, J. (author), Vos, F.M. (author)Image registration of medical images in the presence of large intra-image signal fluctuations is a challenging task. Our paper addresses this problem by introducing a new concept based on the structure tensor of the local phase. The local phase is calculated from the monogenic signal representation of the images. The local phase image is hardly...conference paper 2015
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Shakeri, S.M. (author), Hulsken, B. (author), Van Vliet, L.J. (author), Stallinga, S. (author)Whole Slide Imaging (WSI) systems are used in the emerging field of digital pathology for capturing high-resolution images of tissue slides at high throughput. We present a technique to measure the optical aberrations of WSI systems using a Shack-Hartmann wavefront sensor as a function of field position. The resulting full-field aberration maps...conference paper 2015
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Righolt, C.H. (author), Guffei, A. (author), Knecht, H. (author), Young, I.T. (author), Stallinga, S. (author), Van Vliet, L.J. (author), Mai, S. (author)Advances in light microscopy have enabled the visualization of DNA in the interphase nucleus with more detail than is visible with conventional light microscopy. The nuclear architecture is assumed to be different in cancer cells compared to normal cells. In this paper we have studied, for the first time, the organization of nuclear DNA and that...journal article 2014
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Van Vliet, S. (author), Hol, F.J.H. (author), Weenink, T. (author), Galajda, P. (author), Keymer, J.E. (author)Background Bacterial habitats, such as soil and the gut, are structured at the micrometer scale. Important aspects of microbial life in such spatial ecosystems are migration and colonization. Here we explore the colonization of a structured ecosystem by two neutrally labeled strains of Escherichia coli. Using time-lapse microscopy we studied the...journal article 2014
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Righolt, C.H. (author), Mai, S. (author), Van Vliet, L.J. (author), Stallinga, S. (author)The quality of the reconstructed image in structured illumination microscopy (SIM) depends on various aspects of the image filtering process. To optimize the trade-off between resolution and ringing artifacts, which lead to negative intensities, we extend Lukosz-bound filtering to 3D SIM and derive the parametrization of the 3D SIM cut-off. We...journal article 2014
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Righolt, C.H. (author), Slotman, J.A. (author), Young, I.T. (author), Mai, S. (author), Van Vliet, L.J. (author), Stallinga, S. (author)Various aspects of image filtering affect the final image quality in Structured Illumination Microscopy, in particular the regularization parameter and type of regularization function, the relative height of the side bands, and the shape of the apodization function. We propose an apodization filter without adjustable parameters based on the...journal article 2013
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Kostenko, A. (author), Batenburg, K.J. (author), King, A. (author), Offerman, S.E. (author), Van Vliet, L.J. (author)The reconstruction problem in in-line X-ray Phase-Contrast Tomography is usually approached by solving two independent linearized sub-problems: phase retrieval and tomographic reconstruction. Both problems are often ill-posed and require the use of regularization techniques that lead to artifacts in the reconstructed image. We present a novel...journal article 2013
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Kostenko, A. (author), Batenburg, K.J. (author), Suhonen, H. (author), Offerman, S.E. (author), Van Vliet, L.J. (author)State-of-the-art techniques for phase retrieval in propagation based X-ray phase-contrast imaging are aiming to solve an underdetermined linear system of equations. They commonly employ Tikhonov regularization – an L2-norm regularized deconvolution scheme – despite some of its limitations. We present a novel approach to phase retrieval based on...journal article 2013
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Vulovic, M. (author), Franken, E. (author), Ravelli, R.B.G. (author), Van Vliet, L.J. (author), Rieger, B. (author)Defocus and twofold astigmatism are the key parameters governing the contrast transfer function (CTF) in transmission electron microscopy (TEM) of weak phase objects. We present a new algorithm to estimate these aberrations and the associated uncertainties. Tests show very good agreement between simulated and estimated defocus and astigmatism....journal article 2012
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Kostenko, A. (author), Sharma, H. (author), Gözde Dere, E. (author), King, A. (author), Ludwig, W. (author), Van Oel, W. (author), Offerman, S.E. (author), Stallinga, S. (author), Van Vliet, L.J. (author)This work presents the development of a non-destructive imaging technique for the investigation of the microstructure of cementite grains embedded in a ferrite matrix of medium-carbon steel. The measurements were carried out at the material science beamline of the European Synchrotron Radiation Facility (ESRF) ID11. It was shown that in-line X...conference paper 2011
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Tang, H. (author), Van Walsum, T. (author), Van Onkelen, R.S. (author), Klein, S. (author), Hameeteman, R. (author), Schaap, M. (author), Van den Bouwhuijsen, Q. (author), Witteman, J.C.M. (author), Van der Lugt, A. (author), Van Vliet, L.J. (author), Niessen, W.J. (author)We propose a minimum cost path approach to track the centerlines of the internal and external carotid arteries in multispectral MR data. User interaction is limited to the annotation of three seed points. The cost image is based on both a measure of vessel medialness and lumen intensity similarity in two MRA image sequences: Black Blood MRA and...conference paper 2011
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Voortman, L.M. (author), Stallinga, S. (author), Schoenmakers, R.H.M. (author), Van Vliet, L.J. (author), Rieger, B. (author)Today, the resolution in phase-contrast cryo-electron tomography is for a significant part limited by the contrast transfer function (CTF) of the microscope. The CTF is a function of defocus and thus varies spatially as a result of the tilting of the specimen and the finite specimen thickness. Models that include spatial dependencies have not...journal article 2011
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Caan, M.W.A. (author), Ganesh Khedoe, H. (author), Poot, D.H.J. (author), Den Dekker, A.J. (author), Olabarriaga, S.D. (author), Grimbergen, K.A. (author), Van Vliet, L.J. (author), Vos, F.M. (author)There is an ongoing debate on how to model diffusivity in fiber crossings. We propose an optimization framework for the selection of a dual tensor model and the set of diffusion weighting parameters b, such that both the diffusion shape and orientation parameters can be precisely as well as accurately estimated. For that, we have adopted the...journal article 2010
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Van Wijk, C. (author), Van Ravesteijn, V.F. (author), Vos, F.M. (author), Van Vliet, L.J. (author)Today’s computer aided detection systems for computed tomography colonography (CTC) enable automated detection and segmentation of colorectal polyps.We present a paradigm shift by proposing a method that measures the amount of protrudedness of a candidate object in a scale adaptive fashion. One of the main results is that the performance of the...journal article 2010
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Grigorescu, S.E. (author), Nevo, S.T. (author), Liedenbaum, M.H. (author), Truyen, R. (author), Stoker, J. (author), Van Vliet, L.J. (author), Vos, F.M. (author)Computerized tomographic colonography is a minimally invasive technique for the detection of colorectal polyps and carcinoma. Computer-aided diagnosis (CAD) schemes are designed to help radiologists locating colorectal lesions in an efficient and accurate manner. Large lesions are often initially detected as multiple small objects, due to which...journal article 2010
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Van Ravesteijn, V.F. (author), Van Wijk, C. (author), Vos, F.M. (author), Truyen, R. (author), Peters, J.F. (author), Stoker, J. (author), Van Vliet, L.J. (author)We present a computer-aided detection (CAD) system for computed tomography colonography that orders the polyps according to clinical relevance. TheCADsystem consists of two steps: candidate detection and supervised classification. The characteristics of the detection step lead to specific choices for the classification system. The candidates are...journal article 2010
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Barends, R. (author), Van Vliet, S. (author), Baselmans, J.J.A. (author), Yates, S.J.C. (author), Gao, J.R. (author), Klapwijk, T.M. (author)We present measurements of the quasiparticle relaxation time in Ta superconducting films shaped as planar resonators using the response of the complex conductivity to photon flux. These films have been implanted with magnetic (Mn) as well as non-magnetic atoms (Al). We find a significant decrease of the relaxation time with increasing impurity...conference paper 2009
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Vulovic, M. (author), Rieger, B. (author), Van Vliet, L.J. (author), Koster, A.J. (author), Ravelli, R.B.G. (author)Charge-coupled devices (CCD) are nowadays commonly utilized in transmission electron microscopy (TEM) for applications in life sciences. Direct access to digitized images has revolutionized the use of electron microscopy, sparking developments such as automated collection of tomographic data, focal series, random conical tilt pairs and...journal article 2009
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Van Eekeren, A.W.M. (author), Schutte, K. (author), Van Vliet, L.J. (author)Method of improving the resolution of a small moving object in a digital image sequence comprises the steps of: constructing (101) a high-resolution image background model, detecting (102) the moving object using the high-resolution image background model, fitting (103) a model-based trajectory for object registration, and producing (104) a high...patent 2009
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Van de Giessen, M. (author), Streekstra, G.J. (author), Strackee, S.D. (author), Maas, M. (author), Grimbergen, K.A. (author), Van Vliet, L.J. (author), Vos, F.M. (author)Comparing wrist shapes of different individuals requires alignment of these wrists into the same pose. Unconstrained registration of the carpal bones results in anatomically nonfeasible wrists. In this paper, we propose to constrain the registration using the shapes of adjacent bones, by keeping the width of the gap between adjacent bones...journal article 2009