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Bernd Rieger

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Single molecule localization microscopy with patterned illumination in 3D

Journal article (2023) - P.F. van Velde, P.F. van Velde, B. Rieger, B. Rieger, T.A. Hinsdale, J.P. Cnossen, D. Fan, S. Hung, D. Grunwald, D. Grunwald, C.S. Smith, C.S. Smith, C.S. Smith, C.S. Smith

Three dimensional modulation-enhanced single-molecule localization techniques, such as ModLoc, offer advancements in axial localization precision across the entire field of view and axial capture range, by applying phase shifting to the illumination pattern. However, this impr ...

Edge Enhancement Optimization in Flexible Endoscopic Images to the Perception of Ear, Nose and Throat Professionals

Journal article (2023) - G. Geleijnse, L. L. Veder, M. M. Hakkesteegt, H. H.W. de Gier, B. Rieger, B. Rieger, R. M. Metselaar

Objectives: Digital endoscopes are connected to a video processor that applies various operations to process the image. One of those operations is edge enhancement that sharpens the image. The purpose of this study was to (1) quantify the level of edge enhancement, (2) measure ...

Publisher Correction

3D particle averaging and detection of macromolecular symmetry in localization microscopy (Nature Communications, (2021), 12, 1, (2847), 10.1038/s41467-021-22006-5)

Journal article (2021) - H. Heydarian, M.J. Joosten, B. Rieger, Adrian Przybylski, Florian Schueder, Florian Schueder, Ralf Jungmann, B.J.C. van Werkhoven, Jan Keller-Findeisen, Jonas Ries, S. Stallinga, Mark Bates

The original HTML version of this Article was updated shortly after publication because the previous HTML version linked to an incorrect Supplementary Information file.

@en

Simultaneous orientation and 3D localization microscopy with a Vortex point spread function

Journal article (2021) - C.N. Hulleman, R.Ø. Thorsen, E. Kim, E. Kim, E. Kim, C. Dekker, C. Dekker, S. Stallinga, B. Rieger

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 ...

High-speed multicolor structured illumination microscopy using a hexagonal single mode fiber array

Journal article (2021) - T.A. Hinsdale, S. Stallinga, B. Rieger

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 ...

3D particle averaging and detection of macromolecular symmetry in localization microscopy

Journal article (2021) - H. Heydarian, M.J. Joosten, A. Przybylski, Florian Schueder, Florian Schueder, Ralf Jungmann, Ralf Jungmann, B.J.C. van Werkhoven, J. Keller-Fiendeisen, B. Rieger, S. Stallinga, None More Authors

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 structural ...

Single-crystal copper films on sapphire

Journal article (2020) - G.C.A.M. Janssen, N.M. van der Pers, R.W.A. Hendrikx, A.J. Bottger, C. Kwakernaak, B. Rieger, B. Rieger, M.H.F. Sluiter

Single-crystal copper films on sapphire have recently been reported upon in relation to graphene growth on these films. In the present paper the kinetics of the formation of single crystal copper films is investigated. We demonstrate the importance of heating the sapphire substra ...

Super-resolution fight club

Assessment of 2D and 3D single-molecule localization microscopy software

Journal article (2019) - D Sage, Thanh-An Pham, Hazen Babcock, Tomas Lukes, Thomas Pengo, Ramraj Velmurugan, Alex Herbert, Anurag Agrawal, B. Rieger, None More Authors

With the widespread uptake of 2D and 3D single molecule localization microscopy, a large set of different data analysis packages have been developed to generate super-resolution images. To guide researchers on the optimal analytical software for their experiments, we have designe ...

Publisher Correction

Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software (Nature Methods, (2019), 16, 5, (387-395), 10.1038/s41592-019-0364-4)

Journal article (2019) - Daniel Sage, Thanh-An Pham, Hazen Babcock, Tomas Lukes, Tomas Lukes, Thomas Pengo, Jerry Chao, Ramraj Velmurugan, Alex Herbert, B. Rieger, None More Authors

In the version of this paper originally published, Figure 4a contained errors that were introduced during typesetting. The bottom 11° ThunderSTORM image is an xz view but was incorrectly labeled as xy, and the low x-axis value in the four line profiles was incorrectly set as –60 ...

Single‐Molecule Switching

Fluorescence Polarization Control for On–Off Switching of Single Molecules at Cryogenic Temperatures

Journal article (2018) - C.N. Hulleman, Maximiliaan Huisman, R.J. Moerland, David Grunwald, S. Stallinga, B. Rieger

In article number 1700323, a sparsity‐inducing scheme based on widefield stimulated emission depletion, which requires stringent control of the polarization state of both the excitation and depletion laser, is introduced by Bernd Rieger and co‐workers for superresolution fluoresc ...

Fluorescence Polarization Control for On-Off Switching of Single Molecules at Cryogenic Temperatures

Journal article (2018) - C.N. Hulleman, Maximiliaan Huisman, R.J. Moerland, David Gruenwald, S. Stallinga, B. Rieger

Light microscopy, allowing sub-diffraction-limited resolution, has been among the fastest developing techniques at the interface of biology, chemistry, and physics. Intriguingly no theoretical limit exists on how far the underlying measurement uncertainty can be lowered. In part ...

Image processing and analysis for single-molecule localization microscopy

Computation for nanoscale imaging

Journal article (2015) - B. Rieger, R.P.J. Nieuwenhuizen, S. Stallinga

Fluorescence microscopy is currently the most important tool for visualizing biological structures at the subcellular scale. The combination of fluorescence, which enables a high imaging contrast, and the possibility to apply molecular labeling, which allows for a high imaging sp ...

Contributed

Population difference between L4 and L5 Trojans due to Jupiter's outward migration

A numerical analysis using actual Trojan data

Bachelor thesis (2023) - J.D. Bonenkamp, P.M. Visser, B. Rieger

Ever since their discovery, the Trojans have raised many questions among astrophysicists. In 1989 it was found that there were more L4 than L5 Trojans and the current L4:L5 ratio value is estimated to be 1.6. However, this asymmetry could not be explained by Jupiter’s current orbit and must therefore have arisen during the early development of the Solar System. It was suggested that an outward migration as described by the Nice model could cause the asymmetry. To investigate this, we extended a recent research by modelling an outward migration of Jupiter on the actual Trojans and their symmetric copies. In this manner, we had a broad initial Trojan distribution, which allowed us to investigate several effects of initial values like the Trojan inclinations and maximum angular deviations from the Lagrange point. The simulations used a recently found midpoint Yoshida integrator, which allowed fourth order symplectic simulations for our non-separable Hamiltonian problem. From the simulations it followed that the ratio could only be explained if the Trojans initially had large angular deviations from the Lagrange point, which is possible if they later lost energy due to for example mutual collisions. Also the small initial inclinations as predicted for the early Trojans would in general have risen due to the migration, but it could not explain the the inclinations up to 40 degrees for today Trojans, implying that the increase in inclination must have been caused by other reasons. We found that not only the total migration distance and duration are important, but also the function that describes the evolution of Jupiter’s semi-major axis and the eccentricity of Jupiter’s orbit. For further research we suggest to use data sets on those quantities from simulations with the Nice model, to investigate these related problems together. We believe that our model and code is of great advantage for such a research, because of its optimisations and it allows to implement the data on the distance and eccentricity directly into the model without having to alter the equations of motion.

Coopetition in academia

How competition and cooperation can coexist between academic researchers

Master thesis (2023) - E.S. Berrevoets, E. Kalmar, S.M. Flipse, B. Rieger

Academic research is inherently cooperative, with researchers exchanging information through formal publications as well as direct messaging. Academia are, however, becoming increasingly competitive: limited financial resources and research spots, among other things, may now affe ...

Characterization of a phase camera for the Virgo gravitational wave detector

Master thesis (2023) - F.J. Hoogenberg, M. Fransen, S.F. Pereira, B. Rieger, M.G. van Beuzekom

Gravitational waves predicted by Einstein have been measured in a few observatories worldwide. These detectors are complex interferometers with sizes of kilometers. Misalignments and aberrations in their optical set-up can create higher-order modes in the laser beam. These higher-order mode effects should be compensated to improve the sensitivity of the interferometer. Such a compensating control system requires a real-time wavefront sensor. The phase cameras developed for the Virgo gravitational wave detector can simultaneously create intensity and phase images of the laser wavefront at 11 demodulation frequencies. Currently, the phase images are not used due to difficulties in the interpretation. Therefore, the goal of this research is to improve the understanding of the phase images of a phase camera for the Virgo gravitational wave detector.

A prototype set-up of the phase camera was built at Nikhef. The beam is modulated and sidebands are created such that a beat signal of 80 MHz and the first upper and lower sidebands at 75 and 85 MHz are measured. Images are created by scanning the laser beam across a pinhole diode and digital demodulation. In the chosen optical set-up only one of the two beams that give the measurable beat signal is scanned. This leads to systematic phase effects caused by length differences in the optical path as a function of the scanning angle. To predict the phase images, the interference of two Gaussian beams with a scanning mirror is mathematically derived. Phase images are created with a simulation, which matches within 10 to 20% compared to measurements. To improve the results, the input parameters of the simulation should be measured more accurately and the optical set-up layout should be checked. Also, the phase stability of the prototype set-up is measured. Due to the high sensitivity of the phase camera, very small optical path length differences, for example caused by airflow or temperature differences, lead to significant phase offsets. The long timescale fluctuations in the phase measurements can be reduced by covering the optical set-up. The measured high-frequency phase resolution is Δ𝜙 = 7.1 ± 0.4 mrad and behaves as a function of power as expected.

Dielectric Metasurface Designs for Surface Enhanced Raman Scattering with Large Distances between Nanoparticles

Master thesis (2023) - J.P.A. Dekker, B. Rieger, Giampiero Gerini

In this thesis new dielectric metasurfaces in immersion were explored with a periodic distribution of unit cells with multiple silicon cylinder structures on a reflective gold slab with a fused quartz spacer in between. These new metasurfaces were designed with 60 nm and 130 nm g ...

Fourier Ring Correlation with a single image

Bachelor thesis (2022) - T.M. ten Brink, B. Rieger, P.M. Visser

As super-resolution methods make it possible to capture images at a resolution beyond the diffraction limit, they have no straightforward measure for optical resolution. Consequently, signal-to-noise ratio-based methods to determine resolution such as Fourier Ring Correlation (FR ...

Application of Green's Functions to Self-Gravitating and Rotating Planets

And Modelling the Gravitational Field of the Earth

Bachelor thesis (2020) - L. Koorevaar, R. van der Toorn, D.J. Verschuur, W.G.M. Groenevelt, B. Rieger

A model is designed for solving gravitational profiles of self-gravitating and rotating planets via the use of Poisson's equation for total gravity, i.e., the sum of the gravitational and rotational potential. Poisson's equation is a partial differential equation that is solved w ...

Detecting structural heterogeneity in single-molecule localization microscopy data

Master thesis (2020) - T.A.P.M. Huijben, B. Rieger

For decades, the resolution of fluorescent light microscopy has been bounded by Abbe’s diffraction limit to λ/2NA. Super-resolution methods, awarded with the 2014 Nobel Prize in Chemistry, use tricks to overcome this limit. The general idea is to image blinking fluorophores for a multitude of frames, such that each frame only contains a sparse subset of fluorophores. Assuming that single emitters give rise to a sparse subset of diffraction-limited spots, their locations can be determined with nanometer precision. The resolution of the final reconstructed image is limited by the localization precision and incomplete fluorescent labeling. To even further improve the resolution, by increasing the signal-to-noise and overcoming the problem of a low label- ing density, single-particle averaging can be used if multiple copies of the same target particle (e.g. macro- molecular complex) can be imaged. All emerging localization patterns are computationally merged into one super-superresolution image. Despite the increase in resolution, potential structural variation among the particles will blur the particle fusion result and possible (small) subsets of structurally different particles can- not be detected in the reconstruction. We present an a-priori knowledge-free, unsupervised classification method that splits the dataset into conformationally different groups of images prior to the merging process, which can subsequently be fused per class. The implemented algorithms are validated on multiple exper- imental and simulated datasets. We achieved classification performances of 96% on experimental datasets with up to four different DNA origami structures, are able to detect rare classes of mirrored origami’s occur- ring at a rate of 2%, and capture the variation in the ellipticity of nuclear pore complexes. This new classifica- tion tool will allow microscopists to study heterogeneous samples with single-particle averaging techniques and discriminate between different particles, structures or conformations with a high resolution.

Een ray-tracer voor geodeten van lichtstralen om een zwart gat

Bachelor thesis (2020) - D. Knoppert, P.M. Visser, B. Rieger, B. van den Dries, Y.M. Blanter

In 2019 werd er voor het eerst een foto van een zwart gat gepubliceerd. Het betreffende super zware zwarte gat ligt in het midden van het sterrenstelsel Messier 87. In dit onderzoek willen we simulaties maken van hoe een foto van een zwart gat eruit ziet. Zowel voor een achtergro ...