scholarly journals Intensity-based axial localization approaches for multifocal plane microscopy

2016 ◽  
Author(s):  
Ramraj Velmurugan ◽  
Jerry Chao ◽  
Sripad Ram ◽  
E. Sally Ward ◽  
Raimund J. Ober
Keyword(s):  
Point Source ◽  
Three Dimensional ◽  
Estimation Method ◽  
Location Estimation ◽  
Three Dimensions ◽  
Single Particles ◽  
Localization Accuracy ◽  
Superresolution Microscopy ◽  
Axial Location ◽  
Pixel Location

AbstractMultifocal plane microscopy (MUM) can be used to visualize biological samples in three dimensions over large axial depths and provides for the high axial localization accuracy that is needed in applications such as the three-dimensional tracking of single particles and superresolution microscopy. This report analyzes the performance of intensity-based axial localization approaches as applied to MUM data using Fisher information calculations. In addition, a new non-parametric intensity-based axial location estimation method, Multi-Intensity Lookup Algorithm (MILA), is introduced that, unlike typical intensity-based methods that make use of a single intensity value per data image, utilizes multiple intensity values per data image in determining the axial location of a point source. MILA is shown to be robust against potential bias induced by differences in the sub-pixel location of the imaged point source. The method's effectiveness on experimental data is also evaluated.

scholarly journals Superresolution microscopy reveals the three-dimensional organization of meiotic chromosome axes in intact Caenorhabditis elegans tissue

2017 ◽  
Vol 114 (24) ◽  
pp. E4734-E4743 ◽  
Author(s):  
Simone Köhler ◽  
Michal Wojcik ◽  
Ke Xu ◽  
Abby F. Dernburg
Keyword(s):  
Caenorhabditis Elegans ◽  
Fluorescent Protein ◽  
Germ Line ◽  
Meiotic Chromosome ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Molecular Organization ◽  
Superresolution Microscopy ◽  
Specific Proteins ◽  
Optical Reconstruction

When cells enter meiosis, their chromosomes reorganize as linear arrays of chromatin loops anchored to a central axis. Meiotic chromosome axes form a platform for the assembly of the synaptonemal complex (SC) and play central roles in other meiotic processes, including homologous pairing, recombination, and chromosome segregation. However, little is known about the 3D organization of components within the axes, which include cohesin complexes and additional meiosis-specific proteins. Here, we investigate the molecular organization of meiotic chromosome axes in Caenorhabditis elegans through STORM (stochastic optical reconstruction microscopy) and PALM (photo-activated localization microscopy) superresolution imaging of intact germ-line tissue. By tagging one axis protein (HIM-3) with a photoconvertible fluorescent protein, we established a spatial reference for other components, which were localized using antibodies against epitope tags inserted by CRISPR/Cas9 genome editing. Using 3D averaging, we determined the position of all known components within synapsed chromosome axes to high spatial precision in three dimensions. We find that meiosis-specific HORMA domain proteins span a gap between cohesin complexes and the central region of the SC, consistent with their essential roles in SC assembly. Our data further suggest that the two different meiotic cohesin complexes are distinctly arranged within the axes: Although cohesin complexes containing the kleisin REC-8 protrude above and below the plane defined by the SC, complexes containing COH-3 or -4 kleisins form a central core, which may physically separate sister chromatids. This organization may help to explain the role of the chromosome axes in promoting interhomolog repair of meiotic double-strand breaks by inhibiting intersister repair.

scholarly journals Reconstructing a point source from diffusion fluxes to narrow windows in three dimensions

2021 ◽  
Vol 477 (2253) ◽  
pp. 20210271
Author(s):  
U. Dobramysl ◽  
D. Holcman
Keyword(s):  
Point Source ◽  
Mixed Boundary ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Infinite Domain ◽  
Uniform Distributions ◽  
Stationary Diffusion ◽  
Analytical Formulae ◽  
Stationary Diffusion Equation ◽  
Additive Fluctuations

We develop a computational approach to locate the source of a steady-state gradient of diffusing particles from the fluxes through narrow windows distributed either on the boundary of a three-dimensional half-space or on a sphere. This approach is based on solving the mixed boundary stationary diffusion equation with Neumann–Green’s function. The method of matched asymptotic expansions enables the computation of the probability fluxes. To explore the range of validity of this expansion, we develop a fast analytical-Brownian numerical scheme. This scheme accelerates the simulation time by avoiding the explicit computation of Brownian trajectories in the infinite domain. The results obtained from our derived analytical formulae and the fast numerical simulation scheme agree on a large range of parameters. Using the analytical representation of the particle fluxes, we show how to reconstruct the location of the point source. Furthermore, we investigate the uncertainty in the source reconstruction due to additive fluctuations present in the fluxes. We also study the influence of various window configurations: clustered versus uniform distributions on recovering the source position. Finally, we discuss possible applications for cell navigation in biology.

scholarly journals Three-Dimensional Localization Algorithm of WSN Nodes Based on RSSI-TOA and Single Mobile Anchor Node

2019 ◽  
Vol 2019 ◽  
pp. 1-8 ◽  
Author(s):  
Lieping Zhang ◽  
Zhenyu Yang ◽  
Shenglan Zhang ◽  
Huanhuan Yang
Keyword(s):  
Three Dimensional ◽  
Estimation Method ◽  
Wireless Sensor ◽  
Time Of Arrival ◽  
Localization Algorithm ◽  
Anchor Node ◽  
Localization Accuracy ◽  
Localization Method ◽  
Mobile Anchor ◽  
Mobile Anchor Node

Aimed at the shortcomings of low localization accuracy of the fixed multianchor method, a three-dimensional localization algorithm for wireless sensor network nodes is proposed in this paper, which combines received signal strength indicator (RSSI) and time of arrival (TOA) ranging information and single mobile anchor node. A mobile anchor node was introduced in the proposed three-dimensional localization algorithm for wireless sensor networks firstly, and the mobile anchor node moves according to the Gauss–Markov three-dimensional mobility model. Then, based on the idea of using RSSI ranging in the near end and TOA ranging in the far end, a ranging method combining RSSI and TOA ranging information is proposed to obtain the precise distance between the anchor node and the unknown node. Finally, the maximum-likelihood estimation method is used to estimate the position of unknown nodes based on the obtained ranging values. The MATLAB simulation results show that the proposed algorithm had a higher localization accuracy and lower localization energy consumption compared with the traditional RSSI localization method or TOA localization method.

Characterizing three‐dimensional wavefields with high‐resolution spectra

Geophysics ◽  
1992 ◽  
Vol 57 (4) ◽  
pp. 522-531
Author(s):  
R. A. Meek ◽  
A. A. Vassiliou
Keyword(s):  
Fourier Transform ◽  
Maximum Entropy ◽  
Fourier Transforms ◽  
Spectral Estimation ◽  
Three Dimensional ◽  
Estimation Method ◽  
Synthetic Data ◽  
Estimation Algorithm ◽  
Three Dimensions ◽  
Coherent Noise

Three‐dimensional spectra (frequency‐x‐wavenumber‐y‐wavenumber or [Formula: see text] spectra) can be used to determine the frequency content, velocity, and direction of waves entering an array of receivers. This information is important in detecting aliasing problems, understanding coherent noise, designing arrays, and determining parameters for coherent noise filters. Because of the limited spatial dimensions of most arrays the discrete Fourier transform produces an estimate of the three‐dimensional (3-D) spectrum with severe wavenumber distortion. We extend a 2-D hybrid spectral estimation method to three dimensions by combining a temporal Fourier transform with a spatial 2-D maximum entropy spectral estimation technique. The method produces [Formula: see text] spectra with higher wavenumber resolution and less spectral distortion than corresponding 3-D Fourier spectra. The 2-D maximum entropy spectral estimation algorithm uses a sequence of Fourier transforms to extrapolate the estimated autocorrelation function of the data. We assume the wavenumber spectrum of the data comprises a sum of a few poles. Field and synthetic data are used to demonstrate how 3-D wavefields can be characterized with this method of spectral analysis. From these results we conclude that the method gives excellent wavenumber resolution but performs poorly in detecting small signals in the presence of high amplitude signals. We feel this limitation is not serious for characterizing strong amplitude coherent energy recorded by an array of receivers.

scholarly journals Dynamic triaxial constitutive model for rock subjected to initial stress

Open Physics ◽  
2020 ◽  
Vol 18 (1) ◽  
pp. 149-163
Author(s):  
Junzhe Li ◽  
Guang Zhang ◽  
Mingze Liu ◽  
Shaohua Hu ◽  
Xinlong Zhou
Keyword(s):  
Constitutive Model ◽  
Impact Load ◽  
Three Dimensional ◽  
Estimation Method ◽  
Constant Strain Rate ◽  
Strain Curve ◽  
Initial Pressure ◽  
Expansion Method ◽  
Three Dimensions ◽  
Model Parameters

AbstractBuilding on the existing model, an improved constitutive model for rock is proposed and extended in three dimensions. The model can avoid the defect of non-zero dynamic stress at the beginning of impact loading, and the number of parameters is in a suitable range. The three-dimensional expansion method of the component combination model is similar to that of the Hooke spring, which is easy to operate and understand. For the determination of model parameters, the shared parameter estimation method based on the Levenberg–Marquardt and the Universal Global Optimization algorithm is used, which can be well applied to models with parameters that do not change with confinement and strain rates. According to the established dynamic constitutive equation, the stress–strain curve of rock under the coupling action of the initial hydrostatic pressure load and constant strain-rate impact load can be estimated theoretically. By comparing the theoretical curve with the test data, it is shown that the dynamic constitutive model is suitable for the rock under the initial pressure and impact load.

scholarly journals Real-time multi-parameter spectroscopy and localization in three-dimensional single-particle tracking

2008 ◽  
Vol 6 (suppl_1) ◽  
Author(s):  
Christian Hellriegel ◽  
Enrico Gratton
Keyword(s):  
Laser Scanning ◽  
Three Dimensional ◽  
Single Particle Tracking ◽  
Three Dimensions ◽  
Single Particles ◽  
Ensemble Averaging ◽  
Tracking Technique ◽  
Observation Volume ◽  
Spatio Temporal ◽  
Feedback Algorithm

Tracking of single particles in optical microscopy has been employed in studies ranging from material sciences to biophysics down to the level of single molecules. The technique intrinsically circumvents ensemble averaging and may therefore reveal directly mechanistic details of the involved dynamic processes. Such processes range from translational and rotational motion to spectral dynamics. We distinguish between conventional a posteriori tracking of objects (e.g. from the sequences of images) and the experimentally more refined ‘on-the-fly’ tracking technique. In this technique, the observation volume of the microscope is kept centred with respect to the moving object via a feedback algorithm. This approach brings a series of advantages in comparison with the tracking from images, ranging from a superior spatio-temporal resolution (2–50 nm and 1–32 ms) to the capability of inferring additional data (e.g. fluorescence lifetime, emission spectrum, polarization, intensity dynamics) from an object as it moves over several microns in three dimensions. In this contribution, we describe the principle of the tracking technique as implemented on a two-photon laser scanning microscope and illustrate its capabilities with experimental data, from particles labelled with different dyes moving in a liquid to the characterization of small fluorescently labelled protein assemblies in living cells.

Misalignment Effect on a Three-Dimensional Cruciform Welded Joint

2013 ◽  
Author(s):  
Shuichi Yamatoki ◽  
Seitaro Arimatsu ◽  
Koji Gotoh
Keyword(s):  
Welded Joint ◽  
Three Dimensional ◽  
Estimation Method ◽  
Three Dimensions ◽  
Design Phase ◽  
Misalignment Effect ◽  
Hull Design ◽  
New Equation ◽  
3D Effect ◽  
Modified Equation

In the ship-hull design phase, the distance of a misalignment of a cruciform welded joint is enlarged, by up to 100 mm for example, until its effect is thought to be minimized. To control tolerance, we used a technique to estimate the coefficient of the misalignment effect: the ratio of the stress with misalignment to stress without misalignment. Current methods, created using the two-dimensional (2D) misalignment model and focusing on small misalignments, cannot be applied in the design phase. Misalignment models are needed, as there have been no studies of these joints and it is impractical to do finite element (FE) analysis in each case. We propose an estimation method of the coefficient of misalignment effect in three dimensions (3D). First, we created a new equation to estimate the coefficient in 2D. The equation accommodates larger misalignments. Second, we found the membrane component of a misaligned member stress is reduced as a 3D effect and the coefficient converges given a certain misalignment value. Third, a modified equation taking the effect into account indicates the coefficient in 3D.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

Computer Assisted Image Reconstruction of Oligomer Structure

1976 ◽  
Vol 34 ◽  
pp. 472-473
Author(s):  
A.M. Jones ◽  
A. Max Fiskin
Keyword(s):  
Three Dimensional ◽  
Depth Of Field ◽  
Computer Assisted ◽  
Projection Data ◽  
Two Dimensional ◽  
Single Particles ◽  
Dimensional Reconstruction ◽  
Computer Assisted Image ◽  
The Fourier Transform ◽  
Space Approach

If the tilt of a specimen can be varied either by the strategy of observing identical particles orientated randomly or by use of a eucentric goniometer stage, three dimensional reconstruction procedures are available (l). If the specimens, such as small protein aggregates, lack periodicity, direct space methods compete favorably in ease of implementation with reconstruction by the Fourier (transform) space approach (2). Regardless of method, reconstruction is possible because useful specimen thicknesses are always much less than the depth of field in an electron microscope. Thus electron images record the amount of stain in columns of the object normal to the recording plates. For single particles, practical considerations dictate that the specimen be tilted precisely about a single axis. In so doing a reconstructed image is achieved serially from two-dimensional sections which in turn are generated by a series of back-to-front lines of projection data.

convergent-beam diffraction from surfaces

1987 ◽  
Vol 45 ◽  
pp. 30-33
Author(s):  
J. A. Eades ◽  
A. E. Smith ◽  
D. F. Lynch
Keyword(s):  
Reciprocal Lattice ◽  
Three Dimensional ◽  
Grazing Incidence ◽  
Three Dimensions ◽  
Plane Figure ◽  
Transmission Electron ◽  
Convergent Beam ◽  
Beam Patterns ◽  
Beam Diffraction

It is quite simple (in the transmission electron microscope) to obtain convergent-beam patterns from the surface of a bulk crystal. The beam is focussed onto the surface at near grazing incidence (figure 1) and if the surface is flat the appropriate pattern is obtained in the diffraction plane (figure 2). Such patterns are potentially valuable for the characterization of surfaces just as normal convergent-beam patterns are valuable for the characterization of crystals.There are, however, several important ways in which reflection diffraction from surfaces differs from the more familiar electron diffraction in transmission.GeometryIn reflection diffraction, because of the surface, it is not possible to describe the specimen as periodic in three dimensions, nor is it possible to associate diffraction with a conventional three-dimensional reciprocal lattice.

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