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- Rieger, B. (author), van Vliet, L.J. (author) journal article 2002
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Brinkers, S. (author), Dietrich, H.R.C. (author), De Groote, F.H. (author), Young, I.T. (author), Rieger, B. (author)The wormlike chain model describes the micromechanics of semiflexible polymers by introducing the persistence length. We propose a method of measuring the persistence length of DNA in a controllable near-native environment. Using a dark field microscope, the projected positions of a gold nanoparticle undergoing constrained Brownian motion are...journal article 2009
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Stallinga, S. (author), Rieger, B. (author)The Gaussian function is simple and easy to implement as Point Spread Function (PSF) model for fitting the position of fluorescent emitters in localization microscopy. Despite its attractiveness the appropriateness of the Gaussian is questionable as it is not based on the laws of optics. Here we study the effect of emission dipole orientation in...journal article 2010
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Stallinga, S. (author), Rieger, B. (author)We introduce a method for determining the position and orientation of fixed dipole emitters based on a combination of polarimetry and spot shape detection. A key element is an effective Point Spread Function model based on Hermite functions. The model offers a good description of the shape variations with dipole orientation and polarization...journal article 2012
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- Rieger, B. (author), van den Doel, L.R. (author), van Vliet, L.J. (author) journal article 2003
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Nieuwenhuizen, R.P.J. (author), Nahidiazar, L. (author), Manders, E.M.M. (author), Jalink, K. (author), Stallinga, S. (author), Rieger, B. (author)Co-localization analysis is a widely used tool to seek evidence for functional interactions between molecules in different color channels in microscopic images. Here we extend the basic co-localization analysis by including the orientations of the structures on which the molecules reside. We refer to the combination of co-localization of...journal article 2015
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- Dietrich, H.R.C. (author), Rieger, B. (author), Wiertz, F.G.M. (author), De Groote, F.H. (author), Heering, H.A. (author), Young, I.T. (author), Garini, Y. (author) journal article 2009
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- Nieuwenhuizen, R.P.J. (author), Bates, M. (author), Szymborska, A. (author), Lidke, K.A. (author), Rieger, B. (author), Stallinga, S. (author) journal article 2015
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Nieuwenhuizen, R.P.J. (author), Bates, M. (author), Szymborska, A. (author), Lidke, K.A. (author), Rieger, B. (author), Stallinga, S. (author)Quantification in localization microscopy with reversibly switchable fluorophores is severely hampered by the unknown number of switching cycles a fluorophore undergoes and the unknown stoichiometry of fluorophores on a marker such as an antibody. We overcome this problem by measuring the average number of localizations per fluorophore, or...journal article 2015
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Castaldo, V. (author), Hagen, C.W. (author), Rieger, B. (author), Kruit, P. (author)In principle, a scanning ion microscope can produce smaller probe sizes than a scanning electron microscope because the diffraction contribution is smaller. However, the imaging resolution is often severely limited by the sputtering damage. In this article, an experimental procedure to establish the limit of a focused ion beam system for imaging...journal article 2008
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Broeken, J. (author), Rieger, B. (author), Stallinga, S. (author)We propose a method for simultaneously measuring the position and emission color of single fluorescent emitters based on the use of a large pitch diffraction grating in the emission light path. The grating produces satellite spots adjacent to the main spot; the relative distance between the spots is a measure for the emission wavelength. We...journal article 2014
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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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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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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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Meddens, M.B.M. (author), Rieger, B. (author), Figdor, C.G. (author), Cambi, A. (author), Van den Dries, K. (author)Podosomes are cellular adhesion structures involved in matrix degradation and invasion that comprise an actin core and a ring of cytoskeletal adaptor proteins. They are most often identified by staining with phalloidin, which binds F-actin and therefore visualizes the core. However, not only podosomes, but also many other cytoskeletal structures...journal article 2013
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Selig, B. (author), Vermeer, K.A. (author), Rieger, B. (author), Hillenaar, T. (author), Hendriks, C.L.L. (author)Background Manual and semi-automatic analyses of images, acquired in vivo by confocal microscopy, are often used to determine the quality of corneal endothelium in the human eye. These procedures are highly time consuming. Here, we present two fully automatic methods to analyze and quantify corneal endothelium imaged by in vivo white light slit...journal article 2015
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Löschberger, A. (author), Van de Linde, S. (author), Debauvalle, M.C. (author), Rieger, B. (author), Heilemann, M. (author), Krohne, G. (author), Sauer, M. (author)One of the most complex molecular machines of cells is the nuclear pore complex (NPC), which controls all trafficking of molecules in and out of the nucleus. Because of their importance for cellular processes such as gene expression and cytoskeleton organization, the structure of NPCs has been studied extensively during the last few decades,...journal article 2012
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- Rieger, B. (author), Timmermans, F.J. (author), van Vliet, L.J. (author), Verbeek, P.W. (author) journal article 2004
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Nieuwenhuizen, R.P.J. (author), Nahidiazar, L. (author), Manders, E.M.M. (author), Jalink, K. (author), Stallinga, S. (author), Rieger, B. (author)Co-localization analysis is a widely used tool to seek evidence for functional interactions between molecules in different color channels in microscopic images. Here we extend the basic co-localization analysis by including the orientations of the structures on which the molecules reside. We refer to the combination of co-localization of...journal article 2015
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Hinsdale, T.A. (author), Stallinga, S. (author), Rieger, B. (author)Structured illumination microscopy (SIM) is a widely used imaging technique that doubles the effective resolution of widefield microscopes. Most current implementations rely on diffractive elements, either gratings or programmable devices, to generate structured light patterns in the sample. These can be limited by spectral efficiency, speed, or...journal article 2021