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Haghparast, S. (author), Stallinga, S. (author), Rieger, B. (author)Fusion of multiple chemically identical complexes, so-called particles, in localization microscopy, can improve the signal-to-noise ratio and overcome under-labeling. To this end, structural homogeneity of the data must be assumed. Biological heterogeneity, however, could be present in the data originating from distinct conformational...journal article 2023
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Particle fusion of super-resolution data reveals the unit structure of Nup96 in Nuclear Pore ComplexWang, W. (author), Jakobi, A. (author), Wu, Yu-Le (author), Ries, Jonas (author), Stallinga, S. (author), Rieger, B. (author)Single molecule localization microscopy offers resolution nearly down to the molecular level with specific molecular labelling, and is thereby a promising tool for structural biology. In practice, however, the actual value to this field is limited primarily by incomplete fluorescent labelling of the structure. This missing information can be...journal article 2023
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Wang, W. (author), Jakobi, A. (author), Wu, Yu‑Le ‑L (author), Ries, Jonas (author), Stallinga, S. (author), Rieger, B. (author)Correction to: Scientific Reports, published online 16 August 2023 The original version of this Article contained an error in the upper inset of Figure 4, where the atomic model was missing. The original Figure 4 and accompanying legend appear below. (Figure presented.) Overlay of the fluorophore positions from the SMLM particle fusion data ...journal article 2023
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Hari, S. (author), Slotman, Johan A. (author), Vos, Y. (author), Floris, Christian (author), van Cappellen, W.A. (author), Hagen, C.W. (author), Stallinga, S. (author), Houtsmuller, A.B. (author), Hoogenboom, J.P. (author)Super-resolution fluorescence microscopy can be achieved by image reconstruction after spatially patterned illumination or sequential photo-switching and read-out. Reconstruction algorithms and microscope performance are typically tested using simulated image data, due to a lack of strategies to pattern complex fluorescent patterns with...journal article 2022
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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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Wang, W. (author), Heydarian, H. (author), Huijben, T.A.P.M. (author), Stallinga, S. (author), Rieger, B. (author)Summary: We present a fast particle fusion method for particles imaged with single-molecule localization microscopy. The state-of-the-art approach based on all-to-all registration has proven to work well but its computational cost scales unfavorably with the number of particles N, namely as N2. Our method overcomes this problem and achieves a...journal article 2022
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Kalisvaart, D. (author), Cnossen, J.P. (author), Hung, S. (author), Stallinga, S. (author), Verhaegen, M.H.G. (author), Smith, C.S. (author)Modulation enhanced single-molecule localization microscopy (meSMLM) methods improve the localization precision by using patterned illumination to encode additional position information. Iterative meSMLM (imeSMLM) methods iteratively generate prior information on emitter positions, used to locally improve the localization precision during...journal article 2022
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Siemons, Marijn E. (author), Kapitein, Lukas C. (author), Stallinga, S. (author)Single-molecule localization microscopy has developed into a widely used technique to overcome the diffraction limit and enables 3D localization of single-emitters with nanometer precision. A widely used method to enable 3D encoding is to use a cylindrical lens or a phase mask to engineer the point spread function (PSF). The performance of...journal article 2022
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Stallinga, S. (author), Radmacher, Niels (author), Delon, Antoine (author), Enderlein, Jörg (author)One of the fundamental limits of classical optical microscopy is the diffraction limit of optical resolution. It results from the finite bandwidth of the optical transfer function (or OTF) of an optical microscope, which restricts the maximum spatial frequencies that are transmitted by a microscope. However, given the frequency support of the...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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Hulleman, C.N. (author), Moerland, R.J. (author), Stallinga, S. (author), Rieger, B. (author)With the growing popularity of cryogenic correlative light and electron microscopy, it is becoming increasingly important to bridge the resolution gap between these two modalities. At cryogenic temperatures, the photon yield of fluorophores is a few orders of magnitude higher than at room temperature, enabling localization precisions on the...journal article 2021
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Smith, C.S. (author), Slotman, Johan A. (author), Schermelleh, Lothar (author), Chakrova, N. (author), Hari, S. (author), Vos, Y. (author), Hagen, C.W. (author), Houtsmuller, A.B. (author), Hoogenboom, J.P. (author), Stallinga, S. (author)Super-resolution structured illumination microscopy (SIM) has become a widely used method for biological imaging. Standard reconstruction algorithms, however, are prone to generate noise-specific artifacts that limit their applicability for lower signal-to-noise data. Here we present a physically realistic noise model that explains the...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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Ambrosini, P. (author), Hollemans, Eva (author), Kweldam, Charlotte F. (author), Leenders, Geert J.L.H.van (author), Stallinga, S. (author), Vos, F.M. (author)Cribriform growth patterns in prostate carcinoma are associated with poor prognosis. We aimed to introduce a deep learning method to detect such patterns automatically. To do so, convolutional neural network was trained to detect cribriform growth patterns on 128 prostate needle biopsies. Ensemble learning taking into account other tumor...journal article 2020
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Kner, Peter (author), Manley, Suliana (author), Shechtman, Yoav (author), Stallinga, S. (author)This feature issue commemorating 25 years of STED microscopy and 20 years of SIM is intended to highlight the incredible progress and growth in the field of superresolution microscopy since Stefan Hell and Jan Wichmann published the article Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion...journal article 2020
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van der Graaff, L. (author), Van Leenders, Geert J.L.H. (author), Boyaval, Fanny (author), Stallinga, S. (author)Whole-slide imaging systems can generate full-color image data of tissue slides efficiently, which are needed for digital pathology applications. This paper focuses on a scanner architecture that is based on a multi-line image sensor that is tilted with respect to the optical axis, such that every line of the sensor scans the tissue slide at...journal article 2020
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Cnossen, J.P. (author), Hinsdale, T.A. (author), Thorsen, R.Ø. (author), Siemons, Marijn (author), Schueder, Florian (author), Jungmann, Ralf (author), Smith, C.S. (author), Rieger, B. (author), Stallinga, S. (author)MINFLUX offers a breakthrough in single molecule localization precision, but is limited in field of view. Here we combine centroid estimation and illumination pattern induced photon count variations in a conventional widefield imaging setup to extract position information over a typical micrometer-sized field of view. We show a near two-fold...journal article 2020