Super-resolution microscopy

Summary

Super-resolution microscopy is a series of techniques in optical microscopy that allow such images to have resolutions higher than those imposed by the diffraction limit, which is due to the diffraction of light. Super-resolution imaging techniques rely on the near-field (photon-tunneling microscopy as well as those that use the Pendry Superlens and near field scanning optical microscopy) or on the far-field. Among techniques that rely on the latter are those that improve the resolution only modestly (up to about a factor of two) beyond the diffraction-limit, such as confocal microscopy with closed pinhole or aided by computational methods such as deconvolution or detector-based pixel reassignment (e.g. re-scan microscopy, pixel reassignment), the 4Pi microscope, and structured-illumination microscopy technologies such as SIM and SMI. There are two major groups of methods for super-resolution microscopy in the far-field that can improve the resolution by a much larger factor:

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Official source

https://en.wikipedia.org/wiki/Super-resolution_microscopy

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Fluorescent D-Amino Acids for Super-resolution Microscopy of the Bacterial Cell Wall

Juliette Griffie, Suliana Manley, Jiangtao Qiao, Luc Reymond, Ophélie Rutschmann, Faustine Ambroisine Charline Ryckebusch, Willi Leopold Stepp, Chen Zhang

Fluorescent D-amino acids (FDAAs) have previ-ously been developed to enable in situ highlighting of locations of bacterial cell wall growth. Most bacterial cells lie at the edge of the diffraction limit of visible light; thus, resolving the precise details of peptidoglycan (PG) biosynthesis requires super-resolution micros-copy after probe incorporation. Single molecule localization microscopy (SMLM) has stringent requirements on the fluorophore photophysical properties and therefore has remained challenging in this context. Here, we report the synthesis and characterization of new FDAAs compatible with one-step labeling and SMLM imaging. We demonstrate the incorporation of our probes and their utility for visualizing PG at the nanoscale in Gram-negative, Gram-positive, and mycobacteria species. This improved FDAA toolkit will endow researchers with a nanoscale perspective on the spatial distribution of PG biosynthesis for a broad range of bacterial species.

AMER CHEMICAL SOC2022

Understanding cell functions is the major goal of molecular biology, which intends to elucidate the interactions between biomolecules at a subcellular level. One of the widely used techniques in molecular biology is fluorescence microscopy, which offers high specificity and sensitivity at the submicrometer spatial scale but is limited by diffraction to about 200nm lateral resolution, which is insufficient for the observation of many molecular processes. During the last two decades several super-resolution techniques overcoming the diffraction limit have been developed. However, imaging samples in three dimensions (3D) at high speed remains a challenging and not yet resolved task. This thesis focuses on enhancing super-resolution imaging towards fast, live-cell and 3D imaging. Super-resolution optical fluctuation imaging (SOFI) is a technique based on the stochastic fluctuations of photoswitchable fluorescent markers. It possesses several unique features such as background reduction, capability of increased pixel grid generation, i.e. spatial oversampling, as well as tolerance and robustness to a wide range of photoswitching conditions. In this thesis SOFI was extended to perform 3D analysis. As a result, the resolution in all three spatial dimensions can be improved and the depth sampling increased. We present a novel design of a 3D fluorescence microscope capable of acquiring images of eight depth planes simultaneously. This design incorporates an image-splitting prism, a single optical element allowing to achieve in-depth image separation. The optical performance of the 3D microscope was described and experimentally verified. The simultaneous depth plane acquisition allows to fully exploit the 3D capabilities of SOFI while generating additional virtual depth planes. An algorithm for the extraction of switching kinetics of fluorescent markers is presented. Using appropriate imaging conditions, we demonstrate the applications of 3D SOFI on several examples of fixed and living cells. We also present the potential of the 3D microscope for phase retrieval in transparent samples.

EPFL2017

Super-resolution microscopy live cell imaging and image analysis

Tomas Lukes

Novel fundamental research results provided new techniques going beyond the diffraction limit. These recent advances known as super-resolution microscopy have been awarded by the Nobel Prize as they promise new discoveries in biology and live sciences. All these techniques rely on complex signal and image processing. The applicability in biology, and particularly for live cell imaging, remains challenging and needs further investigation. Focusing on image processing and analysis, the thesis is devoted to a significant enhancement of structured illumination microscopy (SIM) and super-resolution optical fluctuation imaging (SOFI)methods towards fast live cell and quantitative imaging. The thesis presents a novel image reconstruction method for both 2D and 3D SIM data, compatible with weak signals, and robust towards unwanted image artifacts. This image reconstruction is efficient under low light conditions, reduces phototoxicity and facilitates live cell observations. We demonstrate the performance of our new method by imaging long super-resolution video sequences of live U2-OS cells and improving cell particle tracking. We develop an adapted 3D deconvolution algorithm for SOFI, which suppresses noise and makes 3D SOFI live cell imaging feasible due to reduction of the number of required input images. We introduce a novel linearization procedure for SOFI maximizing the resolution gain and show that SOFI and PALM can both be applied on the same dataset revealing more insights about the sample. This PALM and SOFI concept provides an enlarged quantitative imaging framework, allowing unprecedented functional exploration of the sample through the estimation of molecular parameters. For quantifying the outcome of our super-resolutionmethods, the thesis presents a novel methodology for objective image quality assessment measuring spatial resolution and signal to noise ratio in real samples. We demonstrate our enhanced SOFI framework by high throughput 3D imaging of live HeLa cells acquiring the whole super-resolution 3D image in 0.95 s, by investigating focal adhesions in live MEF cells, by fast optical readout of fluorescently labelled DNA strands and by unraveling the nanoscale organization of CD4 proteins on a plasma membrane of T-cells. Within the thesis, unique open-source software packages SIMToolbox and SOFI simulation tool were developed to facilitate implementation of super-resolution microscopy methods.

Czech Technical University in Prague2017

Super-resolution microscopy live cell imaging and image analysis

Tomas Lukes

Czech Technical University in Prague2017

EPFL2017