scholarly journals Off-The-Grid Variational Sparse Spike Recovery: Methods and Algorithms

2021 ◽  
Vol 7 (12) ◽  
pp. 266
Author(s):  
Bastien Laville ◽  
Laure Blanc-Féraud ◽  
Gilles Aubert
Keyword(s):  
Inverse Problem ◽  
Single Molecule ◽  
Super Resolution ◽  
Research Field ◽  
Fine Scale ◽  
Seminal Work ◽  
Resolution Problem ◽  
Localisation Microscopy ◽  
New Research ◽  
Recovery Methods

Gridless sparse spike reconstruction is a rather new research field with significant results for the super-resolution problem, where we want to retrieve fine-scale details from a noisy and filtered acquisition. To tackle this problem, we are interested in optimisation under some prior, typically the sparsity i.e., the source is composed of spikes. Following the seminal work on the generalised LASSO for measures called the Beurling-Lasso (BLASSO), we will give a review on the chief theoretical and numerical breakthrough of the off-the-grid inverse problem, as we illustrate its usefulness to the super-resolution problem in Single Molecule Localisation Microscopy (SMLM) through new reconstruction metrics and tests on synthetic and real SMLM data we performed for this review.

scholarly journals Virtual-'Light-Sheet' Single-Molecule Localisation Microscopy Enables Quantitative Optical Sectioning for Super-Resolution Imaging

PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0125438 ◽  
Author(s):  
Matthieu Palayret ◽  
Helen Armes ◽  
Srinjan Basu ◽  
Adam T. Watson ◽  
Alex Herbert ◽  
...  
Keyword(s):  
Single Molecule ◽  
Super Resolution ◽  
Light Sheet ◽  
Optical Sectioning ◽  
Resolution Imaging ◽  
Localisation Microscopy

scholarly journals NanoJ-SQUIRREL: quantitative mapping and minimisation of super-resolution optical imaging artefacts

2017 ◽  
Author(s):  
Siân Culley ◽  
David Albrecht ◽  
Caron Jacobs ◽  
Pedro Matos Pereira ◽  
Christophe Leterrier ◽  
...  
Keyword(s):  
Single Molecule ◽  
Super Resolution ◽  
Original Data ◽  
Focal Volume ◽  
Coated Pits ◽  
Superresolution Imaging ◽  
Cell Structures ◽  
Image Artefacts ◽  
Localisation Microscopy ◽  
Super Resolution Microscopy

Most super-resolution microscopy methods depend on steps that contribute to the formation of image artefacts. Here we present NanoJ-SQUIRREL, an ImageJ-based analytical approach providing a quantitative assessment of super-resolution image quality. By comparing diffraction-limited images and super-resolution equivalents of the same focal volume, this approach generates a quantitative map of super-resolution defects, as well as methods for their correction. To illustrate its broad applicability to super-resolution approaches we apply our method to Localization Microscopy, STED and SIM images of a variety of in-cell structures including microtubules, poxviruses, neuronal actin rings and clathrin coated pits. We particularly focus on single-molecule localisation microscopy, where super-resolution reconstructions often feature imperfections not present in the original data. By showing the quantitative evolution of data quality over these varied sample preparation, acquisition and super-resolution methods we display the potential of NanoJ-SQUIRREL to guide optimization of superresolution imaging parameters.

scholarly journals Autophagy-Related Proteins GABARAP and LC3B Label Structures of Similar Size but Different Shape in Super-Resolution Imaging

Molecules ◽  
2019 ◽  
Vol 24 (9) ◽  
pp. 1833 ◽  
Author(s):  
Iman Abdollahzadeh ◽  
Johnny Hendriks ◽  
Julia L. Sanwald ◽  
Indra M. Simons ◽  
Silke Hoffmann ◽  
...  
Keyword(s):  
Single Molecule ◽  
Super Resolution ◽  
Vesicular Trafficking ◽  
Hek293 Cells ◽  
Wide Field ◽  
Size Distributions ◽  
Similar Shape ◽  
Resolution Imaging ◽  
Localisation Microscopy ◽  
Related Proteins

Subcellular structures containing autophagy-related proteins of the Atg8 protein family have been investigated with conventional wide-field fluorescence and single molecule localisation microscopy. Fusion proteins of GABARAP and LC3B, respectively, with EYFP were overexpressed in HEK293 cells. While size distributions of structures labelled by the two proteins were found to be similar, shape distributions appeared quite disparate, with EYFP-GABARAP favouring circular structures and elliptical structures being dominant for EYFP-LC3B. The latter also featured a nearly doubled fraction of U-shape structures. The experimental results point towards highly differential localisation of the two proteins, which appear to label structures representing distinct stages or even specific channels of vesicular trafficking pathways. Our data also demonstrate that the application of super-resolution techniques expands the possibilities of fluorescence-based methods in autophagy studies and in some cases can rectify conclusions obtained from conventional fluorescence microscopy with diffraction-limited resolution.

scholarly journals ThX – A next-generation probe for the early detection of amyloid aggregates

2019 ◽  
Author(s):  
Lisa-Maria Needham ◽  
Judith Weber ◽  
Juan A. Varela ◽  
James W. B. Fyfe ◽  
Dung T. Do ◽  
...  
Keyword(s):  
Fluorescent Probe ◽  
Single Molecule ◽  
Protein Misfolding ◽  
Super Resolution ◽  
Fold Increase ◽  
Next Generation ◽  
Aggregation Processes ◽  
Resolution Imaging ◽  
Localisation Microscopy ◽  
Protein Misfolding And Aggregation

AbstractNeurodegenerative diseases such as Alzheimer’s and Parkinson’s are associated with protein misfolding and aggregation. Recent studies suggest that the small, rare and heterogeneous oligomeric species, formed early on in the aggregation process, may be a source of cytotoxicity. Thioflavin T (ThT) is currently the gold-standard fluorescent probe for the study of amyloid proteins and aggregation processes. However, the poor photophysical and binding properties of ThT impairs the study of oligomers. To overcome this challenge, we have designed Thioflavin X, (ThX), a next-generation fluorescent probe which displays superior properties; including a 5-fold increase in brightness and 7-fold increase in binding affinity to amyloidogenic proteins. As an extrinsic dye, this can be used to study unique structural amyloid features both in bulk and on a single-aggregate level. Furthermore, ThX can be used as a super-resolution imaging probe in single-molecule localisation microscopy. Finally, we demonstrate that ThX can be used to detect a distinct oligomeric species, not observed via traditional ThT imaging.

scholarly journals Developing super-resolution fluorescent microscopy for virology research

2021 ◽  
Vol 63 (11) ◽  
pp. 6-12
Author(s):  
Trong Nghia Nguyen ◽  
◽  
Thi Bich Ngoc Nguyen ◽  
Hong Nhung Tran ◽  
Duc Toan Nguyen ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Dengue Virus ◽  
Single Molecule ◽  
Fluorescent Microscopy ◽  
Super Resolution ◽  
Hemorrhagic Fever ◽  
Reconstruction Process ◽  
Virus Particles ◽  
Microscopy Technique ◽  
Localisation Microscopy

Taking advantage of the use of photoswitchable probes and high precision localisation of single molecules to surpass the diffraction limit, super-resolution fluorescence microscopy allows observing non-invasive live-cell at sub-diffraction size (<200 nm). Given the advantage of super-resolution fluorescence microscopy, our group has reconstructed the super-resolution fluorescence microscopybased on the single-molecule localisation microscopy technique with a resolution of 20 nm. In this research, the authors present the reconstruction process of the microscopy system and its application in observing hemorrhagic fever Dengue virus. Dengue virus was cultured in baby hamster kidney (BHK-21) cells and was then negative stained for transmission electron microscope (TEM) or immunofluorescent labeled for stochastic optical reconstruction microscopy (STORM). The diameter of the Dengue virus particles is 45-60 nm measured using TEM and is 84±12 nm measured using STORM. After subtraction of the length of the antibody attached to the virus particles, the diameter of Dengue virus particles measured using STORM are close to which measured using TEM. In conclusion, the authors highlight the findings of super-resolution fluorescence microscopy-based Dengue virus studies and their contributions to the understanding of Dengue virus particles. The current advances in super-resolution microscopy may open new avenues for future virology teaching and research.

scholarly journals Ground-State Depletion Nanoscopy of Nitrogen-Vacancy Centres in Nanodiamonds

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Jelle Storterboom ◽  
Martina Barbiero ◽  
Stefania Castelletto ◽  
Min Gu
Keyword(s):  
Single Molecule ◽  
Ground State ◽  
Nitrogen Concentration ◽  
Super Resolution ◽  
Optical Power ◽  
Stimulated Emission ◽  
Nitrogen Vacancy ◽  
Resolution Imaging ◽  
Localisation Microscopy ◽  
Bulk Diamond

AbstractThe negatively charged nitrogen-vacancy ($${\text{NV}}^{ - }$$ NV - ) centre in nanodiamonds (NDs) has been recently studied for applications in cellular imaging due to its better photo-stability and biocompatibility if compared to other fluorophores. Super-resolution imaging achieving 20-nm resolution of $${\text{NV}}^{ - }$$ NV - in NDs has been proved over the years using sub-diffraction limited imaging approaches such as single molecule stochastic localisation microscopy and stimulated emission depletion microscopy. Here we show the first demonstration of ground-state depletion (GSD) nanoscopy of these centres in NDs using three beams, a probe beam, a depletion beam and a reset beam. The depletion beam at 638 nm forces the $${\text{NV}}^{ - }$$ NV - centres to the metastable dark state everywhere but in the local minimum, while a Gaussian beam at 594 nm probes the $${\text{NV}}^{ - }$$ NV - centres and a 488-nm reset beam is used to repopulate the excited state. Super-resolution imaging of a single $${\text{NV}}^{ - }$$ NV - centre with a full width at half maximum of 36 nm is demonstrated, and two adjacent $${\text{NV}}^{ - }$$ NV - centres separated by 72 nm are resolved. GSD microscopy is here applied to $${\text{NV}}^{ - }$$ NV - in NDs with a much lower optical power compared to bulk diamond. This work demonstrates the need to control the NDs nitrogen concentration to tailor their application in super-resolution imaging methods and paves the way for studies of $${\text{NV}}^{ - }$$ NV - in NDs’ nanoscale interactions.

scholarly journals Super-resolving light fields in microscopy: depth from disparity

2019 ◽  
Author(s):  
Ruth R. Sims ◽  
Sohaib Abdul Rehman ◽  
Martin O. Lenz ◽  
Leila Mureşan ◽  
Kevin O'Holleran
Keyword(s):  
Single Molecule ◽  
Light Field ◽  
Super Resolution ◽  
Depth Of Field ◽  
Source Position ◽  
Multiple Perspective ◽  
Point Emitter ◽  
Simulation And Experiment ◽  
Resolution Imaging ◽  
Localisation Microscopy

Single molecule localisation microscopy (SMLM) has opened a new window for imaging fluorescently labelled biological specimens. Common 3D SMLM techniques enable data collection across an axial range of 1 - 5μm with high precision. Despite the success of 3D single molecule imaging there is a real need to image larger volumes. Here we demonstrate, through simulation and experiment, the potential of Single Molecule Light Field Microscopy (SMLFM) for extended depth-of-field super-resolution imaging, extracting 3D point source position by measuring the disparity between localizations of a point emitter in multiple perspective views.

scholarly journals Laser-free super-resolution microscopy

2017 ◽  
Author(s):  
Kirti Prakash
Keyword(s):  
Single Molecule ◽  
Super Resolution ◽  
Superresolution Microscopy ◽  
Correlative Imaging ◽  
Deep Blue ◽  
Meiotic Chromosomes ◽  
Enhanced Resolution ◽  
Blue Excitation ◽  
Localisation Microscopy ◽  
Super Resolution Microscopy

We report that single-molecule superresolution microscopy can be achieved with a conventional epifluorescence microscope setup and a Mercury arc lamp. The configuration termed as laser-free super-resolution microscopy (LFSM), is an extension of single molecule localisation microscopy (SMLM) techniques and allows single molecules to be switched on and off (a phenomenon termed as “blinking”), detected and localised. The use of a short burst of deep blue excitation (350-380 nm) can be further used to reactivate the blinking, once the blinking process has slowed or stopped. A resolution of 90 nm is achieved on test specimens (mouse and amphibian meiotic chromosomes). Finally, we demonstrate that STED and LFSM can be performed on the same biological sample using a simple imaging medium. It is hoped that this type of correlative imaging will provide a basis for a further enhanced resolution.

scholarly journals Confocal Laser-Scanning Fluorescence-Lifetime Single-Molecule Localisation Microscopy

2020 ◽  
Author(s):  
Jan Christoph Thiele ◽  
Dominic Helmerich ◽  
Nazar Oleksiievets ◽  
Roman Tsukanov ◽  
Eugenia Butkevich ◽  
...  
Keyword(s):  
Single Molecule ◽  
Fluorescence Lifetime ◽  
Spectral Properties ◽  
Laser Scanning ◽  
Super Resolution ◽  
Stimulated Emission ◽  
Laser Scanning Microscopy ◽  
Confocal Laser Scanning ◽  
Confocal Laser ◽  
Localisation Microscopy

AbstractFluorescence lifetime imaging microscopy (FLIM) is an important technique that adds another dimension to the intensity and colour information of conventional microscopy. In particular, it allows for multiplexing fluorescent labels that have otherwise similar spectral properties. Currently, the only super-resolution technique that is capable of recording super-resolved images with lifetime information is STimulated Emission Depletion (STED) microscopy. In contrast, all Single-Molecule Localisation Microscopy (SMLM) techniques that employ wide-field cameras completely lack the lifetime dimension. Here, we combine Fluorescence-Lifetime Confocal Laser-Scanning Microscopy (FL-CLSM) with SMLM for realising single-molecule localisation-based fluorescence-lifetime super-resolution imaging (FL-SMLM). Besides yielding images with a spatial resolution much beyond the diffraction limit, it determines the fluorescence lifetime of all localised molecules. We validate our technique by applying it to direct STochastic Optical Reconstruction Microscopy (dSTORM) and Points Accumulation for Imaging in Nanoscale Topography (PAINT) imaging of fixed cells, and we demonstrate its multiplexing capability on samples with two different labels that differ only by fluorescence lifetime but not by their spectral properties.

Wspólnota semantyczno-leksykalna języków europejskich. O monografii: А.А. Кретов, О.М. Воевудская, И.А. Меркулова, В.Т. Титов, Единство Европы по данным лексики (Воронеж: Издательский дом ВГУ, 2016, ss. 413 [1])

2018 ◽  
Vol 2 (XXIII) ◽  
pp. 121-133
Author(s):  
Katarzyna Wojan
Keyword(s):  
Comparative Research ◽  
Lexical Semantics ◽  
Research Field ◽  
Original Research ◽  
Linguistic Typology ◽  
Lexical Semantic ◽  
Theoretical Linguistics ◽  
Research Concept ◽  
New Research

This article outlines the original research concept developed and applied by the Voronezh researchers, which brought both quantitative and qualitative results to the field of linguistic comparative research. Their monograph is devoted to the macrotypological unity of the lexical semantics of the languages in Europe. In addition, semantic stratification of Russian and Polish lexis has been analyzed. Their research concept is now known as the “lexical-semantic macrotypological school of Voronezh.” Representatives of this school have created a new research field in theoretical linguistics – a lexical-semantic language macrotypology as a branch of linguistic typology. The monograph has been widely discussed and reviewed in Russia.

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