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.

scholarly journals Simulating rhizodeposition patterns around growing and exuding root systems

2021 ◽  
Author(s):  
Magdalena Landl ◽  
Adrian Haupenthal ◽  
Daniel Leitner ◽  
Eva Kroener ◽  
Doris Vetterlein ◽  
...  
Keyword(s):  
Root Architecture ◽  
Three Dimensional ◽  
Temporal Distribution ◽  
Root Systems ◽  
Distribution Patterns ◽  
Three Dimensions ◽  
Root Branching ◽  
Architecture Model ◽  
Spatio Temporal ◽  
Model Approach

1AbstractIn this study, we developed a novel model approach to compute the spatio-temporal distribution patterns of rhizodeposits around growing root systems in three dimensions. This model approach allows us for the first time to study the evolution of rhizodeposition patterns around complex three-dimensional root systems. Root systems were generated using the root architecture model CPlantBox. The concentration of rhizodeposits at a given location in the soil domain was computed analytically. To simulate the spread of rhizodeposits in the soil, we considered rhizodeposit release from the roots, rhizodeposit diffusion into the soil, rhizodeposit sorption to soil particles, and rhizodeposit degradation by microorganisms. To demonstrate the capabilities of our new model approach, we performed simulations for the two example rhizodeposits mucilage and cit-rate and the example root system Vicia faba. The rhizodeposition model was parameterized using values from the literature. Our simulations showed that the rhizosphere soil volume with rhizodeposit concentrations above a defined threshold value (i.e., the rhizodeposit hotspot volume), exhibited a maximum at intermediate root growth rates. Root branching allowed the rhizospheres of individual roots to overlap, resulting in a greater volume of rhizodeposit hotspots. This was particularly important in the case of citrate, where overlap of rhizodeposition zones accounted for more than half of the total rhizodeposit hotspot volumes. Coupling a root architecture model with a rhizodeposition model allowed us to get a better understanding of the influence of root architecture as well as rhizodeposit properties on the evolution of the spatio-temporal distribution patterns of rhizodeposits around growing root systems.

Confocal laser scanning microscopy and Raman imagery of the late Neoproterozoic Chichkan microbiota of South Kazakhstan

2010 ◽  
Vol 84 (3) ◽  
pp. 402-416 ◽  
Author(s):  
J. William Schopf ◽  
Anatoliy B. Kudryavtsev ◽  
Vladimir N. Sergeev
Keyword(s):  
Confocal Laser Scanning Microscopy ◽  
Laser Scanning ◽  
Three Dimensional ◽  
Laser Scanning Microscopy ◽  
Three Dimensions ◽  
Confocal Laser Scanning ◽  
Scanning Microscopy ◽  
Confocal Laser ◽  
Depth Study ◽  
Late Neoproterozoic

Precambrian microbiotas, such as that permineralized in bedded and stromatolitic cherts of the late Neoproterozoic, 750- to 800-Ma-old, Chichkan Formation of South Kazakhstan, have traditionally been studied by optical microscopy only. Such studies, however, are incapable of documenting accurately either the three-dimensional morphology of such fossils or their chemical composition and that of their embedding minerals. As shown here by analyses of fossils of the Chichkan Lagerstätte, the solution to these long-standing problems is provided by two techniques recently introduced to paleontology: confocal laser scanning microscopy (CLSM) and Raman imagery. The two techniques are used together to characterize, in situ and at micron-scale resolution, the cellular and organismal morphology of the thin section-embedded organic-walled Chichkan fossils. In addition, Raman imagery is used to analyze the molecular-structural composition of the carbonaceous fossils and of their embedding mineral matrix, identify the composition of intracellular inclusions, and quantitatively assess the geochemical maturity of the Chichkan organic matter.CLSM and Raman imagery are both broadly applicable to the study of fossils, whether megascopic or microscopic and regardless of mode of preservation, and both are non-intrusive and non-destructive, factors that permit their use for analyses of archived specimens. They are especially useful for the study of microscopic fossils, as is demonstrated in this first in-depth study of diverse taxa of a single Precambrian microbiota for which they provide information in three dimensions at high spatial resolution about their organismal morphology, cellular anatomy, kerogenous composition, mode of preservation, and taphonomy and fidelity of preservation.

scholarly journals Automated Confocal Laser Scanning Microscopy and Semiautomated Image Processing for Analysis of Biofilms

1998 ◽  
Vol 64 (11) ◽  
pp. 4115-4127 ◽  
Author(s):  
Martin Kuehn ◽  
Martina Hausner ◽  
Hans-Joachim Bungartz ◽  
Michael Wagner ◽  
Peter A. Wilderer ◽  
...  
Keyword(s):  
Image Analysis ◽  
Laser Scanning ◽  
Fluorescent Protein ◽  
Image Acquisition ◽  
Three Dimensional ◽  
Laser Scanning Microscopy ◽  
Three Dimensions ◽  
Confocal Laser ◽  
Cross Sectional ◽  
In Situ Conditions

ABSTRACT The purpose of this study was to develop and apply a quantitative optical method suitable for routine measurements of biofilm structures under in situ conditions. A computer program was designed to perform automated investigations of biofilms by using image acquisition and image analysis techniques. To obtain a representative profile of a growing biofilm, a nondestructive procedure was created to study and quantify undisturbed microbial populations within the physical environment of a glass flow cell. Key components of the computer-controlled processing described in this paper are the on-line collection of confocal two-dimensional (2D) cross-sectional images from a preset 3D domain of interest followed by the off-line analysis of these 2D images. With the quantitative extraction of information contained in each image, a three-dimensional reconstruction of the principal biological events can be achieved. The program is convenient to handle and was generated to determine biovolumes and thus facilitate the examination of dynamic processes within biofilms. In the present study, Pseudomonas fluorescens or a green fluorescent protein-expressing Escherichia coli strain, EC12, was inoculated into glass flow cells and the respective monoculture biofilms were analyzed in three dimensions. In this paper we describe a method for the routine measurements of biofilms by using automated image acquisition and semiautomated image analysis.

scholarly journals Historical Underground Structures as 3D Cadastral Objects

2020 ◽  
Vol 12 (10) ◽  
pp. 1547 ◽  
Author(s):  
Agnieszka Bieda ◽  
Jarosław Bydłosz ◽  
Artur Warchoł ◽  
Monika Balawejder
Keyword(s):  
Laser Scanning ◽  
Three Dimensional ◽  
Laser Scanner ◽  
Three Dimensions ◽  
Underground Structures ◽  
The Real Estate ◽  
New Class ◽  
3D Cadastre ◽  
Historical Objects ◽  
Legal Space

The need for accurate registration of underground objects in the 3D cadastre is becoming increasingly common throughout the world. Research studies conducted in this area mostly focus on objects related to transportation or other public utilities and services. However, in settlements with a long history, apart from new objects, there are also various historical objects underground. Such places are not fully discovered, and sometimes they are not even fully inventoried with surveying methods. The aim of this work therefore is to try to describe the possibility of introducing historical undergrounds to the real estate cadastre created for three dimensions, in case of its creation, and to check ground laser scanning as a method of measuring such objects in order to introduce them to the 3D cadastre. Considerations on the inclusion of underground historical objects into the three-dimensional cadastre database began with conceptual considerations. Their result is the elaboration of UML schemas describing relationships among 3D cadastre objects including underground objects. According to the authors, such underground objects should constitute a completely new class called ‘EGB_BuildingBlockUnderground3D’ and be part of the legal space of the entire building represented by the class ‘EGB_BuildingLegalSpace3D’ (the prefix EGB is an acronym of Polish cadastre name ‘Ewidencja Gruntów i Budynków’; in English, it stands for ‘Land and Building Cadastre’). In order to verify in practice the possibility of introducing historical underground objects into the 3D cadastre database, the inventory of the Underground Tourist Route in Rzeszów (Poland) was used. This route consists of a network of underground passageways and cellars built between the 14th and 18th centuries. The measurement was carried out with the application of the Faro Focus 3D terrestrial laser scanner. The underground inventory showed that at the time the current cadastre of land and buildings in Rzeszów was being founded, the boundaries of the cadastral parcels were established without knowing the location of the underground passageways under the Main Market Square. This resulted in a situation in which the objects located underground became parts of more than one cadastral parcel. If a 3D cadastre is created, such a situation must of course be recorded accordingly. The article proposes solutions for such situations.

scholarly journals Asymptotic Distributions for Power Variations of the Solutions to Linearized Kuramoto–Sivashinsky SPDEs in One-to-Three Dimensions

Symmetry ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 73
Author(s):  
Wensheng Wang ◽  
Dazhong Wang
Keyword(s):  
White Noise ◽  
Limit Theorems ◽  
Three Dimensional ◽  
Space Time ◽  
Asymptotic Distributions ◽  
Three Dimensions ◽  
Bifractional Brownian Motion ◽  
Spatio Temporal ◽  
The Relationship ◽  
Time Type

We study the realized power variations for the fourth order linearized Kuramoto–Sivashinsky (LKS) SPDEs and their gradient, driven by the space–time white noise in one-to-three dimensional spaces, in time, have infinite quadratic variation and dimension-dependent Gaussian asymptotic distributions. This class was introduced-with Brownian-time-type kernel formulations by Allouba in a series of articles starting in 2006. He proved the existence, uniqueness, and sharp spatio-temporal Hölder regularity for the above class of equations in d=1,2,3. We use the relationship between LKS-SPDEs and the Houdré–Villaa bifractional Brownian motion (BBM), yielding temporal central limit theorems for LKS-SPDEs and their gradient. We use the underlying explicit kernels and spectral/harmonic analysis to prove our results. On one hand, this work builds on the recent works on the delicate analysis of variations of general Gaussian processes and stochastic heat equation driven by the space–time white noise. On the other hand, it builds on and complements Allouba’s earlier works on the LKS-SPDEs and their gradient.

scholarly journals 3D Roughness Measurement of Failure Surface in CFA Pile Samples Using Three-Dimensional Laser Scanning

2021 ◽  
Vol 11 (6) ◽  
pp. 2713
Author(s):  
Hyungjoon Seo
Keyword(s):  
Point Cloud ◽  
Laser Scanning ◽  
Detection Method ◽  
Three Dimensional ◽  
Point Clouds ◽  
Failure Surface ◽  
Three Dimensions ◽  
Compression Tests ◽  
Mixed Sample ◽  
Three Samples

The bearing capacity of CFA (Continuous Flight Auger) pile is not able to reach the design capacity if proper construction is not performed due to the soil collapse at the bottom of the pile. In this paper, three pile samples were prepared to simulate the bottom of the CFA pile: grouting sample; mixture of grouting and gravel; mixture of grouting and sand. The failure surfaces of each sample obtained by a uniaxial compression tests were represented as a three-dimensional point cloud by three-dimensional laser scanning. Therefore, high resolution of point clouds can be obtained to simulate the failure surfaces of three samples. The three-dimensional point cloud of each failure surface was analyzed by a plane to points histogram (P2PH) method and a roughness detection method by kernel proposed in this paper. These methods can analyze the global roughness as well as the local roughness of the three pile samples in three dimensions. The roughness features of the grouting sample, the mixed sample of grouting and sand, and the mixed sample of grouting and gravel can be distinguished by the sections where points of each sample are predominantly distributed in the histogram of the proposed method.

Photopolymerization and Metalization for Fabricating Functional Devices and Metamaterials

2006 ◽  
Vol 921 ◽  
Author(s):  
Satoshi Kawata ◽  
Takuo Tanaka ◽  
Nobuyuki Takeyasu ◽  
Sana Nakanishi
Keyword(s):  
Laser Scanning ◽  
Negative Refraction ◽  
Photonic Band Gap ◽  
Polymer Surface ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Coil Array ◽  
Lens Array ◽  
Micro Lens Array ◽  
Micro Lens

AbstractWe present three-dimensional micro/nano-fabrication techniques to create new photonic and functional devices. We have demonstrated two-photon-induced photopolymerization for fabricating 3D micro/nano-structures [1, 2]. In this method, arbitrary three-dimensional polymer structures are fabricated by scanning tightly focused infrared femto-second laser in three dimensions. Recently, we extended this technique to fabricate functional micro devices including photonic band-gap crystals [3] and movable micro-springs. The shrinkage of polymer during polymerization is utilized to reduce the structure size beyond the diffraction limit of light [4]. A micro-lens array with 2500 lenses is used to produce a mass of structures in parallel. By using this micro-lens array system, we fabricated 800 micro-springs and micro-cubic structures by single laser scanning [5]. In this presentation, metalization of fabricated polymer structures will also be described. We coat metal on the surface of polymer by electroless metal plating, but not on the glass substrate [6]. Hydrophobic coating was pre-made on the glass substrates and polymer surface is modified with Sn2+-ions. With this method micro-coil array is metalized [7]. Micro-coil array exhibits negative refraction due to the excitation of magnetic field through coils. We would like to show our design of the structure [8]. In the end, we talk about our newly invented diffraction-free imaging with nano metal rod array [9].

“Grid-mapped” freeze-fracture: Three-Dimensional confocal laser scanning microscopy for directed fracturing and histological mapping of neurons in spinal cord and brain

1993 ◽  
Vol 51 ◽  
pp. 64-65
Author(s):  
J. E. Rash ◽  
L. R. Whalen ◽  
P. B. Guthrie ◽  
M. Morita ◽  
R. Dillman ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Laser Scanning ◽  
Three Dimensional ◽  
Freeze Fracture ◽  
Laser Scanning Microscopy ◽  
Three Dimensions ◽  
Male Rats ◽  
Whole Body ◽  
Confocal Laser ◽  
Fracture Plane

A new correlative microscopic technique, “grid-mapped” freeze fracture, is introduced. This technique allows individual cells in histological slices to be freeze fractured, and their ultrastructural details to be correlated with conventional histological and gross anatomical features. Adult male rats were anesthetized, the sciatic nerve was exposed and crushed, and rhodaminefilled latex microspheres (Lumafluor, Inc) were injected at the crush site to label motor neurons. After 3-7 days, rats were fixed by whole-body perfusion. The brains and spinal cords were removed, embedded in 5% gelatin, and 50 or 100 μm thick slices were cut with a Vibratome. Slices were mapped in three-dimensions (Figs. 1-2 and 3-4) using a Molecular Dynamics Multiport 2001 confocal microscope, and the depths of selected cells were measured (±2μm) from the cut surfaces. After freezing on gold specimen supports, the fracture plane was directed through selected neurons using the precise planar microtome of the JEOL JFD-9000-CR freeze-fracture machine.

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.

High-resolution (centimetre-scale) GPS/GIS-based 3D mapping and spatial analysis of in situ fossils in two horned-dinosaur bonebeds in the Dinosaur Park Formation (Upper Cretaceous) at Dinosaur Provincial Park, Alberta, Canada

2020 ◽  
pp. 1-22
Author(s):  
Caleb M. Brown ◽  
Sean Herridge-Berry ◽  
Kentaro Chiba ◽  
Allison Vitkus ◽  
David A. Eberth
Keyword(s):  
Information Systems ◽  
Geographic Information Systems ◽  
High Resolution ◽  
Spatial Data ◽  
Laser Scanning ◽  
Three Dimensional ◽  
Geographic Information ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Digital Map

Mapping of fossil sites represents an important aspect of palaeontology, because the data collected are required for interpreting the taphonomic and depositional history of the site, as well as the palaeoecology and behavior of the organisms. Methods for mapping and documenting certain vertebrate fossil sites, such as trackways, have drastically changed in recent years, with the integrated technologies of photogrammetry, laser scanning, and geographic information systems becoming standard practice, and providing digital, three-dimensional, and georeferenced data for analyses. Contrasting this technological revolution, the methods for mapping vertebrate bone accumulations, such as bonebeds, have changed little in recent decades, and are largely limited to two dimensions, are non-georeferenced, and produce static maps. Here, we present a novel test case in the mapping of two ceratopsid (Dinosauria: Ornithischia) monodominant bonebeds (mass death assemblages) that are documented digitally, fully georeferenced, and in three dimensions, using a combination of high-resolution (at centimetre-scale) global positioning system, photogrammetry, and geographic information systems. Importantly, accompanying spatial data (i.e., size and orientation) are collected in the field in the traditional manner and directly compared with values calculated from the digital map. Parameters describing bone length and orientation exported from the digital map are largely reflective of measured field data, with both size and orientation distributions being statistically indistinguishable, but with disproportionate error for elements smaller than 10 cm. Protocols and methods tested here will hopefully add to the discussion about the future of fossil bonebed mapping, specifically incorporating digital, three-dimensional, and fully georeferenced data into a powerful analytical tool.

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