scholarly journals Particle localization using local gradients and its application to nanometer stabilization of a microscope

2021 ◽  
Author(s):  
Anatolii V. Kashchuk ◽  
Oleksandr Perederiy ◽  
Chiara Caldini ◽  
Lucia Gardini ◽  
Francesco Saverio Pavone ◽  
...  
Keyword(s):  
Single Molecule ◽  
Three Dimensional ◽  
Universal Method ◽  
Superresolution Microscopy ◽  
Accurate Localization ◽  
Micro Particles ◽  
Localization Algorithms ◽  
Gradient Calculation ◽  
Particle Localization ◽  
Local Gradient

Accurate localization of single particles plays an increasingly important role in a range of biological techniques, including single molecule tracking and localization-based superresolution microscopy. Such techniques require fast and accurate particle localization algorithms as well as nanometer-scale stability of the microscope. Here, we present a universal method for three-dimensional localization of single labeled and unlabeled particles based on local gradient calculation of microscopy images. The method outperforms current techniques in high noise conditions, and it is capable of nanometer accuracy localization of nano- and micro-particles with sub-ms calculation time. By localizing a fixed particle as fiducial mark and running a feedback loop, we demonstrate its applicability for active drift correction in sensitive nanomechanical measurements such as optical trapping and superresolution imaging. A multiplatform open software package comprising a set of tools for local gradient calculation in brightfield and fluorescence microscopy is shared to the scientific community.

scholarly journals Obtaining 3D Super-resolution Information from 2D Super-resolution Images through a 2D-to-3D Transformation Algorithm

2017 ◽  
Author(s):  
Andrew Ruba ◽  
Wangxi Luo ◽  
Joseph Kelich ◽  
Weidong Yang
Keyword(s):  
Single Molecule ◽  
Rotational Symmetry ◽  
Three Dimensional ◽  
Super Resolution ◽  
Live Cells ◽  
Limited Information ◽  
Spatiotemporal Resolution ◽  
Superresolution Microscopy ◽  
Localization Analysis ◽  
Probability Information

AbstractCurrently, it is highly desirable but still challenging to obtain three-dimensional (3D) superresolution information of structures in fixed specimens as well as dynamic processes in live cells with a high spatiotemporal resolution. Here we introduce an approach, without using 3D superresolution microscopy or real-time 3D particle tracking, to achieve 3D sub-diffraction-limited information with a spatial resolution of ≤ 1 nm. This is a post-localization analysis that transforms 2D super-resolution images or 2D single-molecule localization distributions into their corresponding 3D spatial probability information. The method has been successfully applied to obtain structural and functional information for 25-300 nm sub-cellular organelles that have rotational symmetry. In this article, we will provide a comprehensive analysis of this method by using experimental data and computational simulations.

scholarly journals A theoretical high-density nanoscopy study leads to the design of UNLOC, an unsupervised algorithm

2018 ◽  
Author(s):  
Sébastien Mailfert ◽  
Jérôme Touvier ◽  
Lamia Benyoussef ◽  
Roxane Fabre ◽  
Asma Rabaoui ◽  
...  
Keyword(s):  
Single Molecule ◽  
Spatial Organization ◽  
Signal To Noise Ratio ◽  
Single Molecules ◽  
High Density ◽  
Superresolution Microscopy ◽  
Central Interest ◽  
Fluorescent Particles ◽  
Particle Localization ◽  
Cramer Rao Bound

ABSTRACTAmong the superresolution microscopy techniques, the ones based on serially imaging sparse fluorescent particles enable the reconstruction of high-resolution images by localizing single molecules. Although challenging, single-molecule localization microscopy (SMLM) methods aim at listing the position of individual molecules leading a proper quantification of the stoichiometry and spatial organization of molecular actors. However, reaching the precision requested to localize accurately single molecules is mainly constrained by the signal-to-noise ratio (SNR) but also the density (Dframe), i.e., the number of fluorescent particles per μm2 per frame. Of central interest, we establish here a comprehensive theoretical study relying on both SNR and Dframe to delineate the achievable limits for accurate SMLM observations. We demonstrate that, for low-density hypothesis (i.e. one-Gaussian fitting hypothesis), any fluorescent particle biases the localization of a particle of interest when they are distant by less than ≈ 600 nm. Unexpectedly, we also report that even dim fluorescent particles should be taken into account to ascertain unbiased localization of any surrounding particles. Therefore, increased Dframe quickly deteriorates the localization precision, the image reconstruction and more generally the quantification accuracy. The first outcome is a standardized density-SNR space diagram to determine the achievable SMLM resolution expected with experimental data. Additionally, this study leads to the identification of the essential requirements for implementing UNLOC (UNsupervised particle LOCalization), an unsupervised and fast computing algorithm approaching the Cramér-Rao bound for particles at high-density per frame and without any prior on their intensity. UNLOC is available as an ImageJ plugin.

scholarly journals Novel fibrillar structure in the inversin compartment of primary cilia revealed by 3D single-molecule superresolution microscopy

2020 ◽  
Vol 31 (7) ◽  
pp. 619-639 ◽  
Author(s):  
Henrietta W. Bennett ◽  
Anna-Karin Gustavsson ◽  
Camille A. Bayas ◽  
Petar N. Petrov ◽  
Nancie Mooney ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Cell Lines ◽  
Single Molecule ◽  
Primary Cilia ◽  
Three Dimensional ◽  
Fibrillar Structure ◽  
Systematic Analysis ◽  
Superresolution Microscopy ◽  
Superresolution Imaging

Using three-dimensional single-molecule superresolution imaging and systematic analysis of knockout cell lines, we have determined the molecular structure and composition of the inversin compartment in primary cilia. INVS establishes fibrillar structures that recruit ANKS6-NEK8 complexes to sequester NPHP3 in this unique periaxonemal compartment.

FINAL VERSION.pdf

2019 ◽  
Author(s):  
Nasir Saeed ◽  
Mohamed-Slim Alouini ◽  
Tareq Y. Al-Naffouri
Keyword(s):  
Graph Partitioning ◽  
Three Dimensional ◽  
Smart Objects ◽  
Localization Technique ◽  
Optical Internet ◽  
Spectral Graph ◽  
Accurate Localization ◽  
Spectral Graph Partitioning ◽  
Link Connectivity

<div>Localization is a fundamental task for optical internet</div><div>of underwater things (O-IoUT) to enable various applications</div><div>such as data tagging, routing, navigation, and maintaining link connectivity. The accuracy of the localization techniques for OIoUT greatly relies on the location of the anchors. Therefore, recently localization techniques for O-IoUT which optimize the anchor’s location are proposed. However, optimization of anchors location for all the smart objects in the network is not a useful solution. Indeed, in a network of densely populated smart objects, the data collected by some sensors are more valuable than the data collected from other sensors. Therefore, in this paper, we propose a three-dimensional accurate localization technique by optimizing the anchor’s location for a set of smart objects. Spectral graph partitioning is used to select the set of valuable</div><div>sensors.</div>

Accuracy analysis of BLE beacon-based localization in smart buildings

2021 ◽  
pp. 1-20
Author(s):  
Rosen Ivanov
Keyword(s):  
Use Case ◽  
Accuracy Analysis ◽  
Localization Algorithm ◽  
Computing Power ◽  
Smart Buildings ◽  
Localization Accuracy ◽  
Positioning Systems ◽  
Deployment Strategy ◽  
Accurate Localization ◽  
Localization Algorithms

The majority of services that deliver personalized content in smart buildings require accurate localization of their clients. This article presents an analysis of the localization accuracy using Bluetooth Low Energy (BLE) beacons. The aim is to present an approach to create accurate Indoor Positioning Systems (IPS) using algorithms that can be implemented in real time on platforms with low computing power. Parameters on which the localization accuracy mostly depends are analyzed: localization algorithm, beacons’ density, deployment strategy, and noise in the BLE channels. An adaptive algorithm for pre-processing the signals from the beacons is proposed, which aims to reduce noise in beacon’s data and to capture visitor’s dynamics. The accuracy of five range-based localization algorithms in different use case scenarios is analyzed. Three of these algorithms are specially designed to be less sensitive to noise in radio channels and require little computing power. Experiments conducted in a simulated and real environment show that using proposed algorithms the localization accuracy less than 1 m can be obtained.

scholarly journals 3D monitoring of the surface slippage effect on micro-particle sedimentation by digital holographic microscopy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Majid Panahi ◽  
Ramin Jamali ◽  
Vahideh Farzam Rad ◽  
Mojtaba Khorasani ◽  
Ahamd Darudi ◽  
...  
Keyword(s):  
Slip Length ◽  
Particle Interaction ◽  
Three Dimensional ◽  
Digital Holographic Microscopy ◽  
Particle Sedimentation ◽  
Micro Particles ◽  
Slippage Effect ◽  
Holographic Microscopy ◽  
3D Information ◽  
Experimental Findings

AbstractIn several phenomena in biology and industry, it is required to understand the comprehensive behavior of sedimenting micro-particles in fluids. Here, we use the numerical refocusing feature of digital holographic microscopy (DHM) to investigate the slippage effect on micro-particle sedimentation near a flat wall. DHM provides quantitative phase contrast and three-dimensional (3D) imaging in arbitrary time scales, which suggests it as an elegant approach to investigate various phenomena, including dynamic behavior of colloids. 3D information is obtained by post-processing of the recorded digital holograms. Through analysis of 3D trajectories and velocities of multiple sedimenting micro-particles, we show that proximity to flat walls of higher slip lengths causes faster sedimentation. The effect depends on the ratio of the particle size to (1) the slip length and (2) its distance to the wall. We corroborate our experimental findings by a theoretical model which considers both the proximity and the particle interaction to a wall of different hydrophobicity in the hydrodynamic forces.

scholarly journals Three-dimensional ultrasonic trapping of micro-particles in water with a simple and compact two-element transducer

2017 ◽  
Vol 111 (9) ◽  
pp. 094101 ◽  
Author(s):  
A. Franklin ◽  
A. Marzo ◽  
R. Malkin ◽  
B. W. Drinkwater
Keyword(s):  
Three Dimensional ◽  
Micro Particles

scholarly journals Parallel, linear, and subnanometric 3D tracking of microparticles with Stereo Darkfield Interferometry

2021 ◽  
Vol 7 (6) ◽  
pp. eabe3902
Author(s):  
Martin Rieu ◽  
Thibault Vieille ◽  
Gaël Radou ◽  
Raphaël Jeanneret ◽  
Nadia Ruiz-Gutierrez ◽  
...  
Keyword(s):  
High Precision ◽  
High Throughput ◽  
Single Molecule ◽  
Particle Tracking ◽  
Focal Plane ◽  
Tracking System ◽  
Three Dimensional ◽  
3D Tracking ◽  
Single Molecule Force Spectroscopy ◽  
A New Technique

While crucial for force spectroscopists and microbiologists, three-dimensional (3D) particle tracking suffers from either poor precision, complex calibration, or the need of expensive hardware, preventing its massive adoption. We introduce a new technique, based on a simple piece of cardboard inserted in the objective focal plane, that enables simple 3D tracking of dilute microparticles while offering subnanometer frame-to-frame precision in all directions. Its linearity alleviates calibration procedures, while the interferometric pattern enhances precision. We illustrate its utility in single-molecule force spectroscopy and single-algae motility analysis. As with any technique based on back focal plane engineering, it may be directly embedded in a commercial objective, providing a means to convert any preexisting optical setup in a 3D tracking system. Thanks to its precision, its simplicity, and its versatility, we envision that the technique has the potential to enhance the spreading of high-precision and high-throughput 3D tracking.

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