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Thorsen, R.Ø. (author), Hulleman, C.N. (author), Rieger, B. (author), Stallinga, S. (author)
Combining orientation estimation with localization microscopy opens up the possibility to analyze the underlying orientation of biomolecules on the nanometer scale. Inspired by the recent improvement of the localization precision by shifting excitation patterns (MINFLUX, SIMFLUX), we have adapted the idea towards the modulation of excitation...
journal article 2022
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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
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Hulleman, C.N. (author), Thorsen, R.Ø. (author), Kim, E. (author), Dekker, C. (author), Stallinga, S. (author), Rieger, B. (author)
Estimating the orientation and 3D position of rotationally constrained emitters with localization microscopy typically requires polarization splitting or a large engineered Point Spread Function (PSF). Here we utilize a compact modified PSF for single molecule emitter imaging to estimate simultaneously the 3D position, dipole orientation, and...
journal article 2021
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Huijben, T.A.P.M. (author), Heydarian, H. (author), Auer, Alexander (author), Schueder, Florian (author), Jungmann, Ralf (author), Stallinga, S. (author), Rieger, B. (author)
Particle fusion for single molecule localization microscopy improves signal-to-noise ratio and overcomes underlabeling, but ignores structural heterogeneity or conformational variability. We present a-priori knowledge-free unsupervised classification of structurally different particles employing the Bhattacharya cost function as dissimilarity...
journal article 2021
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Heydarian, H. (author), Joosten, M.J. (author), Przybylski, A. (author), Schueder, Florian (author), Jungmann, Ralf (author), van Werkhoven, B.J.C. (author), Keller-Fiendeisen, J. (author), Rieger, B. (author), Stallinga, S. (author)
Single molecule localization microscopy offers in principle resolution down to the molecular level, but in practice this is limited primarily by incomplete fluorescent labeling of the structure. This missing information can be completed by merging information from many structurally identical particles. In this work, we present an approach for 3D...
journal article 2021
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Li, Q. (author), Hulleman, C.N. (author), Moerland, R.J. (author), Mailvaganam, Elil (author), Ganapathy, S. (author), Brinks, D. (author), Stallinga, S. (author), Rieger, B. (author)
Total internal reflection fluorescence (TIRF) microscopy is an important imaging tool for the investigation of biological structures, especially the study on cellular events near the plasma membrane. Imaging at cryogenic temperatures not only enables observing structures in a near-native and fixed state but also suppresses irreversible photo...
journal article 2021
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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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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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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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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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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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