Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Precise Three-Dimensional Scan-Free Multiple-Particle Tracking over Large Axial Ranges with Tetrapod Point Spread Functions.

ABSTRACT: We employ a novel framework for information-optimal microscopy to design a family of point spread functions (PSFs), the Tetrapod PSFs, which enable high-precision localization of nanoscale emitters in three dimensions over customizable axial (z) ranges of up to 20 μm with a high numerical aperture objective lens. To illustrate, we perform flow profiling in a microfluidic channel and show scan-free tracking of single quantum-dot-labeled phospholipid molecules on the surface of living, thick mammalian cells.

SUBMITTER: Shechtman Y

PROVIDER: S-EPMC4462996 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Precise Three-Dimensional Scan-Free Multiple-Particle Tracking over Large Axial Ranges with Tetrapod Point Spread Functions.

Shechtman Yoav Y Weiss Lucien E LE Backer Adam S AS Sahl Steffen J SJ Moerner W E WE

Nano letters 20150518 6

We employ a novel framework for information-optimal microscopy to design a family of point spread functions (PSFs), the Tetrapod PSFs, which enable high-precision localization of nanoscale emitters in three dimensions over customizable axial (z) ranges of up to 20 μm with a high numerical aperture objective lens. To illustrate, we perform flow profiling in a microfluidic channel and show scan-free tracking of single quantum-dot-labeled phospholipid molecules on the surface of living, thick mamma ...[more]

PMID: 25939423

Similar Datasets

Microscopic scan-free surface profiling over extended axial ranges by point-spread-function engineering.

Project description:The shape of a surface, i.e., its topography, influences many functional properties of a material; hence, characterization is critical in a wide variety of applications. Two notable challenges are profiling temporally changing structures, which requires high-speed acquisition, and capturing geometries with large axial steps. Here, we leverage point-spread-function engineering for scan-free, dynamic, microsurface profiling. The presented method is robust to axial steps and acquires full fields of view at camera-limited framerates. We present two approaches for implementation: fluorescence-based and label-free surface profiling, demonstrating the applicability to a variety of sample geometries and surface types.

| S-EPMC7608779 | biostudies-literature

Axial localization and tracking of self-interference nanoparticles by lateral point spread functions.

Project description:Sub-diffraction limited localization of fluorescent emitters is a key goal of microscopy imaging. Here, we report that single upconversion nanoparticles, containing multiple emission centres with random orientations, can generate a series of unique, bright and position-sensitive patterns in the spatial domain when placed on top of a mirror. Supported by our numerical simulation, we attribute this effect to the sum of each single emitter's interference with its own mirror image. As a result, this configuration generates a series of sophisticated far-field point spread functions (PSFs), e.g. in Gaussian, doughnut and archery target shapes, strongly dependent on the phase difference between the emitter and its image. In this way, the axial locations of nanoparticles are transferred into far-field patterns. We demonstrate a real-time distance sensing technology with a localization accuracy of 2.8 nm, according to the atomic force microscope (AFM) characterization values, smaller than 1/350 of the excitation wavelength.

| S-EPMC8016974 | biostudies-literature

Tracking the extensive three-dimensional motion of single ions by an engineered point-spread function.

Project description:Three-dimensional (3D) imaging of individual atoms is a critical tool for discovering new physical phenomena and developing new technologies in microscopic systems. However, the current single-atom-resolved 3D imaging methods are limited to static circumstances or a shallow detection range. Here, we demonstrate a generic dynamic 3D imaging method to track the extensive motion of single ions by exploiting the engineered point-spread function (PSF). We show that the image of a single ion can be engineered into a helical PSF, thus enabling single-snapshot acquisition of the position information of the ion in the trap. A preliminary application of this technique is demonstrated by recording the 3D motion trajectory of a single trapped ion and reconstructing the 3D dynamical configuration transition between the zig and zag structures of a 5-ion crystal. This work opens the path for studies on single-atom-resolved dynamics in both trapped-ion and neutral-atom systems.

| S-EPMC11294470 | biostudies-literature

Three-dimensional tracking of single mRNA particles in Saccharomyces cerevisiae using a double-helix point spread function.

Project description:Optical imaging of single biomolecules and complexes in living cells provides a useful window into cellular processes. However, the three-dimensional dynamics of most important biomolecules in living cells remains essentially uncharacterized. The precise subcellular localization of mRNA-protein complexes plays a critical role in the spatial and temporal control of gene expression, and a full understanding of the control of gene expression requires precise characterization of mRNA transport dynamics beyond the optical diffraction limit. In this paper, we describe three-dimensional tracking of single mRNA particles with 25-nm precision in the x and y dimensions and 50-nm precision in the z dimension in live budding yeast cells using a microscope with a double-helix point spread function. Two statistical methods to detect intermittently confined and directed transport were used to quantify the three-dimensional trajectories of mRNA for the first time, using ARG3 mRNA as a model. Measurements and analysis show that the dynamics of ARG3 mRNA molecules are mostly diffusive, although periods of non-Brownian confinement and directed transport are observed. The quantitative methods detailed in this paper can be broadly applied to the study of mRNA localization and the dynamics of diverse other biomolecules in a wide variety of cell types.

| S-EPMC2964242 | biostudies-literature

Three-dimensional tracking using a single-spot rotating point spread function created by a multiring spiral phase plate.

Project description:SignificanceThree-dimensional (3D) imaging and object tracking is critical for medical and biological research and can be achieved by multifocal imaging with diffractive optical elements (DOEs) converting depth ( z ) information into a modification of the two-dimensional image. Physical insight into DOE designs will spur this expanding field.AimTo precisely track microscopic fluorescent objects in biological systems in 3D with a simple low-cost DOE system.ApproachWe designed a multiring spiral phase plate (SPP) generating a single-spot rotating point spread function (SS-RPSF) in a microscope. Our simple, analytically transparent design process uses Bessel beams to avoid rotational ambiguities and achieve a significant depth range. The SPP was inserted into the Nomarski prism slider of a standard microscope. Performance was evaluated using fluorescent beads and in live cells expressing a fluorescent chromatin marker.ResultsBead localization precision was <25 nm in the transverse dimensions and ≤70 nm along the axial dimension over an axial range of 6 μm . Higher axial precision ( ≤50 nm ) was achieved over a shallower focal depth of 2.9 μm . 3D diffusion constants of chromatin matched expected values.ConclusionsPrecise 3D localization and tracking can be achieved with a SS-RPSF SPP in a standard microscope with minor modifications.

| S-EPMC9799159 | biostudies-literature

Real-time nanomicroscopy via three-dimensional single-particle tracking.

Project description:We developed a new method for real-time, three-dimensional tracking of fluorescent particles. The instrument is based on a laser-scanning confocal microscope where the focus of the laser beam is scanned or orbited around the particle. Two confocal pinholes are used to simultaneously monitor regions immediately above and below the particle and a feedback loop is used to keep the orbit centered on the particle. For moderate count rates, this system can track particles with 15 nm spatial resolution in the lateral dimensions and 50 nm in the axial dimension at a temporal resolution of 32 ms. To investigate the interaction of the tracked particles with cellular components, we have combined our orbital tracking microscope with a dual-color, wide-field setup. Dual-color fluorescence wide-field images are recorded simultaneously in the same image plane as the particle being tracked. The functionality of the system was demonstrated by tracking fluorescent-labeled artificial viruses in tubulin-eGFP expressing HUH7 cells. The resulting trajectories can be used to investigate the microtubule network with super resolution.

| S-EPMC2857558 | biostudies-literature

Fast Three-Dimensional Single-Particle Tracking in Natural Brain Tissue.

Project description:Observation of molecular dynamics is often biased by the optical very heterogeneous environment of cells and complex tissue. Here, we have designed an algorithm that facilitates molecular dynamic analyses within brain slices. We adjust fast astigmatism-based three-dimensional single-particle tracking techniques to depth-dependent optical aberrations induced by the refractive index mismatch so that they are applicable to complex samples. In contrast to existing techniques, our online calibration method determines the aberration directly from the acquired two-dimensional image stream by exploiting the inherent particle movement and the redundancy introduced by the astigmatism. The method improves the positioning by reducing the systematic errors introduced by the aberrations, and allows correct derivation of the cellular morphology and molecular diffusion parameters in three dimensions independently of the imaging depth. No additional experimental effort for the user is required. Our method will be useful for many imaging configurations, which allow imaging in deep cellular structures.

| S-EPMC4601043 | biostudies-literature

Three-dimensional spatiotemporal tracking of fluorine-18 radiolabeled yeast cells via positron emission particle tracking.

Project description:A method for Positron Emission Particle Tracking (PEPT) based on optical feature point identification techniques is demonstrated for use in low activity tracking experiments. A population of yeast cells of approximately 125,000 members is activated to roughly 55 Bq/cell by 18F uptake. An in vitro particle tracking experiment is performed with nearly 20 of these cells after decay to 32 Bq/cell. These cells are successfully identified and tracked simultaneously in this experiment. This work extends the applicability of PEPT as a cell tracking method by allowing a number of cells to be tracked together, and demonstrating tracking for very low activity tracers.

| S-EPMC5500330 | biostudies-literature

Reference ranges for three-dimensional feature tracking cardiac magnetic resonance: comparison with two-dimensional methodology and relevance of age and gender.

Project description:Myocardial deformation is a sensitive marker of sub-clinical myocardial dysfunction that carries independent prognostic significance across a broad range of cardiovascular diseases. It is now possible to perform 3D feature tracking of SSFP cines on cardiac magnetic resonance imaging (FT-CMR). This study provides reference ranges for 3D FT-CMR and assesses its reproducibility compared to 2D FT-CMR. One hundred healthy individuals with 10 men and women in each of 5 age deciles from 20 to 70 years, underwent 2D and 3D FT-CMR of left ventricular myocardial strain and strain rate using SSFP cines. Good health was defined by the absence of hypertension, diabetes, obesity, dyslipidaemia, or any cardiovascular, renal, hepatic, haematological and systemic inflammatory disease. Normal values for myocardial strain assessed by 3D FT-CMR were consistently lower compared with 2D FT-CMR measures [global circumferential strain (GCS) 3D - 17.6 ± 2.6% vs. 2D - 20.9 ± 3.7%, P < 0.005]. Validity of 3D FT-CMR was confirmed against other markers of systolic function. The 3D algorithm improved reproducibility compared to 2D, with GCS having the best inter-observer agreement [intra-class correlation (ICC) 0.88], followed by global radial strain (GRS; ICC 0.79) and global longitudinal strain (GLS, ICC 0.74). On linear regression analyses, increasing age was weakly associated with increased GCS (R2 = 0.15, R = 0.38), peak systolic strain rate, peak late diastolic strain rate, and lower peak early systolic strain rate. 3D FT-CMR offers superior reproducibility compared to 2D FT-CMR, with circumferential strain and strain rates offering excellent intra- and inter-observer variability. Normal range values for myocardial strain measurements using 3D FT-CMR are provided.

| S-EPMC5889420 | biostudies-literature

Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model.

Project description:The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical and thoraco-lumbar regions. In the course of our studies concerning the evolution of Hox gene regulation, we produced a transgenic mouse model expressing fish Hox genes, which displayed a reduced number of thoraco-lumbar vertebrae and concurrent sacral homeotic transformations. Here, we analyze this mutant stock and conclude that the ancestral, pre-tetrapodial Hox code already possessed the capacity to induce vertebrae with sacral characteristics. This suggests that alterations in the interpretation of the Hox code may have participated to the evolution of this region in tetrapods, along with potential modifications of the HOX proteins themselves. With its reduced vertebral number, this mouse stock violates a previously described developmental constraint, which applies to the thoraco-lumbar region. The resulting offset between motor neuron morphology, vertebral patterning and the relative positioning of hind limbs illustrates that the precise orchestration of the Hox-clock in parallel with other ontogenetic pathways places constraints on the evolvability of the body plan.

| S-EPMC4678112 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data