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Wilding, D. (author), Pozzi, P. (author), Soloviev, O.A. (author), Vdovin, Gleb (author), Verhaegen, M.H.G. (author)Three-dimensional microscopy suffers from sample-induced aberrations that reduce the resolution and lead to misinterpretations of the object distribution. In this paper, the resolution of a three-dimensional fluorescent microscope is significantly improved by introducing an amplitude diversity in the form of a binary amplitude mask positioned...journal article 2018
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Piscaer, P.J. (author), Gupta, A. (author), Soloviev, O.A. (author), Verhaegen, M.H.G. (author)In this paper, we propose the use of Gaussian radial basis functions (GRBFs) to model the generalized pupil function for phase retrieval. The selection of the GRBF hyper-parameters is analyzed to achieve an increased accuracy of approximation. The performance of the GRBF-based method is compared in a simulation study with another modal-based...journal article 2018
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Kazasidis, Orestis (author), Verpoort, Sven (author), Soloviev, O.A. (author), Vdovin, Gleb (author), Verhaegen, M.H.G. (author), Wittrock, Ulrich (author)With a view to the next generation of large space telescopes, we investigate guide-starfree, image-based aberration correction using a unimorph deformable mirror in a plane conjugate to the primary mirror.We designed and built a high-resolution imaging testbed to evaluate control algorithms. In this paper we use an algorithm based on the...journal article 2018
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Agbana, T.E. (author), Diehl, J.C. (author), van Pul, Fiona (author), Khan, Shahid M. (author), Patlan, Vsevolod (author), Verhaegen, M.H.G. (author), Vdovin, Gleb (author)We have optimized the design and imaging procedures, to clearly resolve the malaria parasite in Giemsa-stained thin blood smears, using simple low-cost cellphone-based microscopy with oil immersion. The microscope uses a glass ball as the objective and the phone camera as the tube lens. Our optimization includes the optimal choice of the ball...journal article 2018
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Wills, Adrian (author), Yu, C. (author), Ljung, Lennart (author), Verhaegen, M.H.G. (author)Using Maximum Likelihood (or Prediction Error) methods to identify linear state space model is a prime technique. The likelihood function is a nonconvex function and care must be exercised in the numerical maximization. Here the focus will be on affine parameterizations which allow some special techniques and algorithms. Three approaches to...journal article 2018
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Pozzi, P. (author), Soloviev, O.A. (author), Wilding, D. (author), Vdovin, Gleb (author), Verhaegen, M.H.G. (author)We report on a universal sample-independent sensorless adaptive optics method, based on modal optimization of the second moment of the fluorescence emission from a point-like excitation. Our method employs a sample-independent precalibration, performed only once for the particular system, to establish the direct relation between the image...journal article 2018
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Wilding, D. (author), Pozzi, P. (author), Soloviev, O.A. (author), Vdovin, Gleb (author), Fiolka, Reto (author), Verhaegen, M.H.G. (author)The light-sheet fluorescence microscopy is an excellent tool for the investigation of large three dimensional microscopy samples at the cellular level, however, the ability to resolve features is strongly affected by the presence of scattering and aberrations. These effects are two fold in light-sheet microscopy, as the illumination path...conference paper 2018
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Gedon, Daniel (author), Piscaer, P.J. (author), Batselier, K. (author), Smith, C.S. (author), Verhaegen, M.H.G. (author)An extension of the Tensor Network (TN) Kalman filter [2], [3] for large scale LTI systems is presented in this paper. The TN Kalman filter can handle exponentially large state vectors without constructing them explicitly. In order to have efficient algebraic operations, a low TN rank is required. We exploit the possibility to approximate the...conference paper 2019
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Piscaer, P.J. (author), Soloviev, O.A. (author), Verhaegen, M.H.G. (author)A new wavefront sensorless adaptive optics method is presented that can accurately correct for time-varying aberrations using a single focal plane image at each sample instance. The linear relation between the mean square of the aberration gradient and the change in second moment of the image forms the basis of the presented method. The new...journal article 2019
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Pozzi, P. (author), Maddalena, L. (author), Ceffa, N.G. (author), Soloviev, O.A. (author), Vdovin, Gleb (author), Carroll, E.C.M. (author), Verhaegen, M.H.G. (author)The use of spatial light modulators to project computer generated holograms is a common strategy for optogenetic stimulation of multiple structures of interest within a three-dimensional volume. A common requirement when addressing multiple targets sparsely distributed in three dimensions is the generation of a points cloud, focusing excitation...journal article 2019
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Doelman, R. (author), Verhaegen, M.H.G. (author)A rank-constrained reformulation of the blind deconvolution problem on images taken with coherent illumination is proposed. Since in the reformulation the rank constraint is imposed on a matrix that is affine in the decision variables, we propose a novel convex heuristic for the blind deconvolution problem. The proposed heuristic allows for...journal article 2019
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Doelman, R. (author), Klingspor, Måns (author), Hansson, Anders (author), Löfberg, Johan (author), Verhaegen, M.H.G. (author)To optimally compensate for time-varying phase aberrations with adaptive optics, a model of the dynamics of the aberrations is required to predict the phase aberration at the next time step. We model the time-varying behavior of a phase aberration, expressed in Zernike modes, by assuming that the temporal dynamics of the Zernike coefficients...journal article 2019
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Nguyen, Hieu Thao (author), Bui, Hoa T. (author), Nguyen, Duy Cuong (author), Verhaegen, M.H.G. (author)Motivated by a number of questions concerning transversality-type properties of pairs of sets recently raised by Ioffe and Kruger, this paper reports several new characterizations of the intrinsic transversality property in Hilbert spaces. New results in terms of normal vectors clarify the picture of intrinsic transversality, its variants and...journal article 2020
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Piscaer, P.J. (author), Soloviev, O.A. (author), Verhaegen, M.H.G. (author)This paper discusses various practical problems arising in the design and simulation of predictive control methods for adaptive optics. Although there has been increased attention towards optimal prediction and control methods for AO systems, they are often tested in simplified simulation environments. The use of advanced AO simulators...conference paper 2020
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Agbana, T.E. (author), Nijman, Patrick (author), Hoeboer, M.D.B. (author), van Grootheest, D.N. (author), van Diepen, Angela (author), van Lieshout, Lisette (author), Diehl, J.C. (author), Verhaegen, M.H.G. (author), Vdovin, Gleb (author)We present a simple method for the diagnosis of urinary schistosomiasis using an in-line lensless holographic microscope combined with flow cytometry technique. Using simple image processing algorithms and binary image classifier, our system provides automated detection of Schistosoma haematobium eggs in infected urine samples. Registered...conference paper 2020
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Yu, C. (author), Ljung, Lennart (author), Wills, Adrian (author), Verhaegen, M.H.G. (author)In this paper, a unified identification framework called constrained subspace method for structured state-space models (COSMOS) is presented, where the structure is defined by a user specified linear or polynomial parametrization. The new approach operates directly from the input and output data, which differs from the traditional two-step...journal article 2020
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Haber, Aleksandar (author), Verhaegen, M.H.G. (author)To develop high-performance controllers for adaptive optics (AO) systems, it is essential to first derive sufficiently accurate state-space models of deformable mirrors (DMs). However, it is often challenging to develop realistic large-scale finite element (FE) state-space models that take into account the system damping, actuator dynamics,...journal article 2020
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Heemels, Alex (author), Agbana, T.E. (author), Pereira, S.F. (author), Diehl, J.C. (author), Verhaegen, M.H.G. (author), Vdovin, Gleb (author)Fourier Ptychography is a computational imaging technique able to decouple high resolution from wide field of view, bypassing the diffraction limit of the microscope. Since it does not rely on high precision mechanics or fluorescent imaging, it is of practical interest for implementation in low scale devices. Despite its gains, realizing a...conference paper 2020
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Pozzi, P. (author), Smith, C.S. (author), Carroll, E.C.M. (author), Wilding, D. (author), Soloviev, O.A. (author), Booth, Martin (author), Vdovin, Gleb (author), Verhaegen, M.H.G. (author)Inhomogeneities in the refractive index of a biological microscopy sample can introduce phase aberrations, severely impairing the quality of images. Adaptive optics can be employed to correct for phase aberrations and improve image quality. However, conventional adaptive optics can only correct a single phase aberration for the whole field of...journal article 2020
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Nguyen, Hieu Thao (author), Soloviev, O.A. (author), Verhaegen, M.H.G. (author)We present an efficient phase retrieval approach for imaging systems with high numerical aperture based on the vectorial model of the point spread function. The algorithm is in the class of alternating minimization methods and can be adjusted for applications with either known or unknown amplitude of the field in the pupil. The algorithm...journal article 2020