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 polarization to enhance the orientation precision. For this modality two modes are analyzed: i) normally incident excitation with three polarization steps to retrieve the in-plane angle of emitters and ii) obliquely incident excitation with p-polarization with five different azimuthal angles of incidence to retrieve the full orientation. Firstly, we present a theoretical study of the lower precision limit with a Cramér-Rao bound for these modes. For the oblique incidence mode we find a favorable isotropic orientation precision for all molecular orientations if the polar angle of incidence is equal to arccos ^√2/3 ≈ 35 degrees. Secondly, a simulation study is performed to assess the performance for low signal-to-background ratios and how inaccurate illumination polarization angles affect the outcome. We show that a precision, at the Cramér-Rao bound (CRB) limit, of just 2.4 and 1.6 degrees in the azimuthal and polar angles can be achieved with only 1000 detected signal photons and 10 background photons per pixel (about twice better than reported earlier). Lastly, the alignment and calibration of an optical microscope with polarization control is described in detail. With this microscope a proof-of-principle experiment is carried out, demonstrating an experimental in-plane precision close to the CRB limit for signal photon counts ranging from 400 to 10,000.

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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-bleaching rates, resulting in increased photo-stability of fluorophores. Traditional TIRF microscopes produce an evanescent field based on high numerical aperture immersion objective lenses with high magnification, which results in a limited field of view and is incompatible with cryogenic conditions. Here, we present a waveguide-based TIRF microscope, which is able to generate a uniform evanescent field using high refractive index waveguides on photonic chips and to obtain cellular observation at cryogenic temperatures. Our method provides an inexpensive way to achieve total-internal-reflection fluorescence imaging under cryogenic conditions.

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Localization microscopy has circumvented the diffraction limit by sequentially imaging individual light emitting molecules at a time. The position of these individual molecules can be determined and a super-resolution reconstruction is made with improved resolution. Normally freely rotating emitters are used such that the point spread function (PSF) is rotationally symmetric and only minor errors in the localization process are made by approximating the PSF with a Gaussian. The precision with which the individual emitters can be localized scales with the 1/√N, N the number of detected photons so that more detected photons leads to a better localization precision. However, the emission of fluorescent molecules is limited by photobleaching, a light induced chemical reaction to a permanent non-fluorescent state. In this thesis we investigate the effect of cooling the sample to cryogenic temperatures with liquid nitrogen. This reduces the chemical reaction rates and improves photostability more than 100 fold. To use localization microscopy it is necessary to switch the fluorescent molecules between an on-state and off-state, this turns out to be difficult at cryogenic temperatures. Standard methods used at room temperature in aqueous media do not work. As the molecules are frozen in place at cryogenic temperatures we use polarized light to selectively image molecules with certain orientations at a time. To realize this it is necessary to generate pure linear polarization with an arbitrary orientation in the sample plane. By calibrating the phase difference induced by the dichroic mirrors this can be achieved, effectively modulating the fluorescence of fixed dipole emitters at cryogenic temperatures. The addition of an orthogonal linearly polarized stimulated emission depletion (STED) beam narrows the orientational distribution of fluorescing molecules. This method does induce some degree of sparsity, however, it is not enough for localization microscopy of dense biological samples. Furthermore, the STED process reduces the photon yield of single molecules. This is presumably caused by the long dark-state recovery measured on fluorescent molecules in vacuum and at cryogenic temperatures. Localization microscopy of fixed or orientationally constrained emitters has long been avoided as the orientation of individual molecules leads to bias in the localizations. There are various ways to eliminate this bias but they reduce the amount of information that can be extracted from the sample. By fixing the orientation of fluorescent emitters to biomolecules of interest they become reporters for the orientation of the biomolecules. We have devised the so-called Vortex PSF with which the orientation, 3D position and degree of rotational constraint can be extracted from a single image. Alternatively the orientation of single-molecules can be probed with varying polarization states over multiple frames achieving a better precision with less photons. @en

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 Ångström scale. The current challenge is to induce sparsity at cryogenic temperatures such that individual fluorescent molecules can be localized. In this paper, we demonstrate the progress of using polarized stimulated-emission depletion (STED) to induce sparsity at cryogenic temperatures and in vacuum. We generate linear polarization of arbitrary in-plane orientations to achieve polarized STED with a sparsity of 3.3:1. Furthermore, we have probed the dark-state lifetime of ATTO 647N at cryogenic temperatures and in vacuum at room temperature. This dark state in vacuum is long-lived (τ=38 ms) and could be the cause for reduced photostability of fluorophores under STED illumination in vacuum. The experiments were done on an in-house designed and built liquid nitrogen cryostat, enabling 30 hours of stable cryogenic fluorescence microscopy.

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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 degree of rotational constraint from a single 2D image. We use an affordable and commonly available phase plate, normally used for STED microscopy in the excitation light path, to alter the PSF in the emission light path. This resulting Vortex PSF does not require polarization splitting and has a compact PSF size, making it easy to implement and combine with localization microscopy techniques. In addition to a vectorial PSF fitting routine we calibrate for field-dependent aberrations which enables orientation and position estimation within 30% of the Cramér-Rao bound limit over a 66 μm field of view. We demonstrate this technique on reorienting single molecules adhered to the cover slip, λ-DNA with DNA intercalators using binding-activated localization microscopy, and we reveal periodicity on intertwined structures on supercoiled DNA.@en

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 particular data fusion of large amounts of images can reduce the measurement error to match the reso-lution of structural methods like cryo-electron microscopy. Fluorescence, although reliant on a reporter molecule and therefore not the first choice to obtain ultraresolution structures, brings highly specific labeling of molecules in a large assembly to the table and inherently allows the detection of multiple colors, which enables the interrogation of multiple molecular species at the same time in the same sample. Here, the problems to be solved in the coming years, with the aim of higher resolution, are discussed, and what polarization depletion of fluorescence at cryogenic temperatures can contribute for fluorescence imaging of biological samples, like whole cells, is described.@en

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 fluorescence microscopy. The ideal state involves excitation and depletion lasers with linear polarizations, orthogonally oriented in the sample plane. This state is obtained from linearly polarized light from the laser, which is made elliptically polarized before reflecting off the dichroic mirror. @en

Single Molecule Localization Microscopy has become one of the most successful and widely applied methods of Super‐resolution Fluorescence Microscopy. Its achievable resolution strongly depends on the number of detectable photons from a single molecule until photobleaching. By cooling a sample from room temperature down to liquid nitrogen temperatures, the photostability of dyes can be enhanced by more than 100 fold, which results in an improvement in localization precision greater than 10 times. Here, we investigate a variety of fluorescent dyes in the red spectral region, and we find an average photon yield between 3.5 ⋅ 106 to 11 ⋅ 106 photons before bleaching at liquid nitrogen temperatures, corresponding to a theoretical localization precision around 0.1 nm. @en

Recently, Franke, Sauer and van de Linde introduced a way to estimate the axial position of single-molecules (TRABI). To this end, they compared the detected photon count from a temporal radial-aperture-based intensity estimation to the estimated count from Gaussian point-spread function (PSF) fitting to the data. Empirically they found this photometric ratio to be around 0.7-0.8 close to focus and decreasing away from it. Here, we explain this reported but unexplained discrepancy and furthermore show that the photometric ratio as indicator for axial position is susceptible even to typical optical aberrations.@en

Point spread function (PSF) engineering is used in single emitter localization to measure the emitter position in 3D and possibly other parameters such as the emission color or dipole orientation as well. Advanced PSF models such as spline fits to experimental PSFs or the vectorial PSF model can be used in the corresponding localization algorithms in order to model the intricate spot shape and deformations correctly. The complexity of the optical architecture and fit model makes PSF engineering approaches particularly sensitive to optical aberrations. Here, we present a calibration and alignment protocol for fluorescence microscopes equipped with a spatial light modulator (SLM) with the goal of establishing a wavefront error well below the diffraction limit for optimum application of complex engineered PSFs.We achieve high-precision wavefront control, to a level below 20 mλ wavefront aberration over a 30 minute time window after the calibration procedure, using a separate light path for calibrating the pixel-to-pixel variations of the SLM, and alignment of the SLM with respect to the optical axis and Fourier plane within 3 μm (x/y) and 100 μm (z) error. Aberrations are retrieved from a fit of the vectorial PSF model to a bead z-stack and compensated with a residual wavefront error comparable to the error of the SLM calibration step. This well-calibrated and corrected setup makes it possible to create complex '3D+λ' PSFs that fit very well to the vectorial PSF model. Proof-of-principle bead experiments show precisions below 10 nm in x, y, and λ, and below 20 nm in z over an axial range of 1 μm with 2000 signal photons and 12 background photons.

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