scholarly journals Three-dimensional reconstruction of the fast-start swimming kinematics of densely schooling fish

2011 ◽  
Vol 9 (66) ◽  
pp. 77-88 ◽  
Author(s):  
Sachit Butail ◽  
Derek A. Paley
Keyword(s):  
Cross Sections ◽  
Tracking System ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Verbal Cues ◽  
Elliptical Cross ◽  
Fish School ◽  
Schooling Fish ◽  
Dimensional Reconstruction ◽  
Fast Start

Information transmission via non-verbal cues such as a fright response can be quantified in a fish school by reconstructing individual fish motion in three dimensions. In this paper, we describe an automated tracking framework to reconstruct the full-body trajectories of densely schooling fish using two-dimensional silhouettes in multiple cameras. We model the shape of each fish as a series of elliptical cross sections along a flexible midline. We estimate the size of each ellipse using an iterated extended Kalman filter. The shape model is used in a model-based tracking framework in which simulated annealing is applied at each step to estimate the midline. Results are presented for eight fish with occlusions. The tracking system is currently being used to investigate fast-start behaviour of schooling fish in response to looming stimuli.

Three-dimensional reconstruction of metabolic data from quantitative autoradiography of rat brain

1984 ◽  
Vol 247 (3) ◽  
pp. E412-E419 ◽  
Author(s):  
L. S. Hibbard ◽  
R. A. Hawkins
Keyword(s):  
High Speed ◽  
Three Dimensional ◽  
Image Data ◽  
Brain Structures ◽  
Three Dimensions ◽  
Quantitative Autoradiography ◽  
Alignment Algorithm ◽  
Computer Methods ◽  
Mathematical Properties ◽  
Dimensional Reconstruction

Quantitative autoradiography is a powerful method for studying brain function by the determination of blood flow, glucose utilization, or transport of essential nutrients. Autoradiographic images contain vast amounts of potentially useful information, but conventional analyses can practically sample the data at only a small number of points arbitrarily chosen by the experimenter to represent discrete brain structures. To use image data more fully, computer methods for its acquisition, storage, quantitative analysis, and display are required. We have developed a system of computer programs that performs these tasks and has the following features: 1) editing and analysis of single images using interactive graphics, 2) an automatic image alignment algorithm that places images in register with one another using only the mathematical properties of the images themselves, 3) the calculation of mean images from equivalent images in different experimental serial image sets, 4) the calculation of difference images (e.g., experiment-minus-control) with the option to display only differences estimated to be statistically significant, and 5) the display of serial image metabolic maps reconstructed in three dimensions using a high-speed computer graphics system.

scholarly journals Computational Study of Zigzag Spacer Design with Elliptical Cross-Section Filaments

2020 ◽  
Vol 307 ◽  
pp. 01047
Author(s):  
Gohar Shoukat ◽  
Farhan Ellahi ◽  
Muhammad Sajid ◽  
Emad Uddin
Keyword(s):  
Mass Transfer ◽  
Cross Section ◽  
Cross Sections ◽  
Computational Study ◽  
Flow Direction ◽  
Three Dimensional ◽  
Circular Cross Section ◽  
Two Dimensional ◽  
Permeate Flux ◽  
Elliptical Cross

The large energy consumption of membrane desalination process has encouraged researchers to explore different spacer designs using Computational Fluid Dynamics (CFD) for maximizing permeate per unit of energy consumed. In previous studies of zigzag spacer designs, the filaments are modeled as circular cross sections in a two-dimensional geometry under the assumption that the flow is oriented normal to the filaments. In this work, we consider the 45° orientation of the flow towards the three-dimensional zigzag spacer unit, which projects the circular cross section of the filament as elliptical in a simplified two-dimensional domain. OpenFOAM was used to simulate the mass transfer enhancement in a reverse-osmosis desalination unit employing spiral wound membranes lined with zigzag spacer filaments. Properties that impact the concentration polarization and hence permeate flux were analyzed in the domain with elliptical filaments as well as a domain with circular filaments to draw suitable comparisons. The range of variation in characteristic parameters across the domain between the two different configurations is determined. It was concluded that ignoring the elliptical projection of circular filaments to the flow direction, can introduce significant margin of error in the estimation of mass transfer coefficient.

scholarly journals Investigation of microvascular morphological measures for skeletal muscle tissue oxygenation by image-based modelling in three dimensions

2017 ◽  
Vol 14 (135) ◽  
pp. 20170635 ◽  
Author(s):  
B. Zeller-Plumhoff ◽  
K. R. Daly ◽  
G. F. Clough ◽  
P. Schneider ◽  
T. Roose
Keyword(s):  
Skeletal Muscle ◽  
Muscle Tissue ◽  
Cross Sections ◽  
Tissue Oxygenation ◽  
Volume Fraction ◽  
Three Dimensional ◽  
Capillary Density ◽  
Three Dimensions ◽  
Two Dimensional ◽  
Contrast Imaging

The supply of oxygen in sufficient quantity is vital for the correct functioning of all organs in the human body, especially for skeletal muscle during exercise. Traditionally, microvascular oxygen supply capability is assessed by the analysis of morphological measures on transverse cross-sections of muscle, e.g. capillary density or capillary-to-fibre ratio. In this work, we investigate the relationship between microvascular structure and muscle tissue oxygenation in mice. Phase contrast imaging was performed using synchrotron radiation computed tomography (SR CT) to visualize red blood cells (RBCs) within the microvasculature in mouse soleus muscle. Image-based mathematical modelling of the oxygen diffusion from the RBCs into the muscle tissue was subsequently performed, as well as a morphometric analysis of the microvasculature. The mean tissue oxygenation was then compared with the morphological measures of the microvasculature. RBC volume fraction and spacing (mean distance of any point in tissue to the closest RBC) emerged as the best predictors for muscle tissue oxygenation, followed by length density (summed RBC length over muscle volume). The two-dimensional measures of capillary density and capillary-to-fibre ratio ranked last. We, therefore, conclude that, in order to assess the states of health of muscle tissue, it is advisable to rely on three-dimensional morphological measures rather than on the traditional two-dimensional measures.

scholarly journals Automatic Three-Dimensional Reconstruction of Fascicles in Peripheral Nerves from Histological Images

2020 ◽  
Author(s):  
Daniel Tovbis ◽  
Anne Agur ◽  
Jeremy P.M. Mogk ◽  
José Zariffa
Keyword(s):  
Peripheral Nerve ◽  
Cross Sections ◽  
Peripheral Nerves ◽  
Active Contours ◽  
Three Dimensional ◽  
Dimensional Reconstruction ◽  
Histological Images ◽  
Hematoxylin And Eosin ◽  
Fully Automatic ◽  
Neural Anatomy

AbstractComputational studies can be used to support the development of peripheral nerve interfaces, but currently use simplified models of nerve anatomy, which may impact the applicability of simulation results. To better quantify and model neural anatomy across the population, we have developed an algorithm to automatically reconstruct accurate peripheral nerve models from histological cross-sections. We acquired serial median nerve cross-sections from human cadaveric samples, staining one set with hematoxylin and eosin (H&E) and the other using immunohistochemistry (IHC) with anti-neurofilament antibody. We developed a four-step processing pipeline involving registration, fascicle detection, segmentation, and reconstruction. We compared the output of each step to manual ground truths, and additionally compared the final models to commonly used extrusions, via intersection-over-union (IOU). Fascicle detection and segmentation required the use of a neural network and active contours in H&E-stained images, but only simple image processing methods for IHC-stained images. Reconstruction achieved an IOU of 0.42±0.07 for H&E and 0.37±0.16 for IHC images, with errors partially attributable to global misalignment at the registration step, rather than poor reconstruction. This work provides a quantitative baseline for fully automatic construction of peripheral nerve models. Our models provided fascicular shape and branching information that would be lost via extrusion.

scholarly journals Three-dimensional structure of the Z band in a normal mammalian skeletal muscle.

1996 ◽  
Vol 133 (3) ◽  
pp. 571-583 ◽  
Author(s):  
J P Schroeter ◽  
J P Bretaudiere ◽  
R L Sass ◽  
M A Goldstein
Keyword(s):  
Skeletal Muscle ◽  
Cross Sections ◽  
Three Dimensional ◽  
Square Lattice ◽  
Actin Binding ◽  
Dimensional Structure ◽  
Mammalian Skeletal Muscle ◽  
Axial Filament ◽  
Three Dimensional Structure ◽  
Dimensional Reconstruction

The three-dimensional structure of the vertebrate skeletal muscle Z band reflects its function as the muscle component essential for tension transmission between successive sarcomeres. We have investigated this structure as well as that of the nearby I band in a normal, unstimulated mammalian skeletal muscle by tomographic three-dimensional reconstruction from electron micrograph tilt series of sectioned tissue. The three-dimensional Z band structure consists of interdigitating axial filaments from opposite sarcomeres connected every 18 +/- 12 nm (mean +/- SD) to one to four cross-connecting Z-filaments are observed to meet the axial filaments in a fourfold symmetric arrangement. The substantial variation in the spacing between cross-connecting Z-filament to axial filament connection points suggests that the structure of the Z band is not determined solely by the arrangement of alpha-actinin to actin-binding sites along the axial filament. The cross-connecting filaments bind to or form a "relaxed interconnecting body" halfway between the axial filaments. This filamentous body is parallel to the Z band axial filaments and is observed to play an essential role in generating the small square lattice pattern seen in electron micrographs of unstimulated muscle cross sections. This structure is absent in cross section of the Z band from muscles fixed in rigor or in tetanus, suggesting that the Z band lattice must undergo dynamic rearrangement concomitant with crossbridge binding in the A band.

Three-dimensional reconstruction of a mammalian Z-band from skeletal muscle

1992 ◽  
Vol 50 (1) ◽  
pp. 542-543
Author(s):  
J. P. Schroeter ◽  
M. A. Goldstein ◽  
J. P. Bretaudiere ◽  
R. L. Sass
Keyword(s):  
Skeletal Muscle ◽  
Cross Sections ◽  
Three Dimensional ◽  
Square Lattice ◽  
Back Projection ◽  
Axial Filament ◽  
Dimensional Reconstruction ◽  
Rat Soleus Muscle ◽  
Tilt Series ◽  
Three Dimensional Models

We have completed 3-d reconstructions of several regions of the Z-band in relaxed rat soleus muscle using the method of weighted back projection on a tilt series from two different longitudinal sections. Various displays of the reconstructions were interpreted after corrections for section shrinkage and comparisons to three dimensional models. Examination of cross-sections of the reconstructed Z-bands reveal that the lattice is in the small square form. We have previously shown that this form of the Z-band lattice is predominate in relaxed skeletal muscle. The reconstructions reveal that cross-connecting Z-filaments are arranged in opposing pairs along the axial filament. Successive pairs of filaments are rotated by ninety degrees about the axial filament, thus generating the four-fold appearance seen in the projected small square lattice.

Ultrasonic Reflectivity Imaging in Three Dimensions: Reconstruction with Spherical Transducer Arrays

1979 ◽  
Vol 1 (3) ◽  
pp. 210-231 ◽  
Author(s):  
Stephen J. Norton ◽  
Melvin Linzer
Keyword(s):  
Signal To Noise Ratio ◽  
Acoustic Pulse ◽  
Cutoff Frequency ◽  
Three Dimensional ◽  
Point Sources ◽  
Three Dimensions ◽  
Reconstruction Process ◽  
Dimensional Reconstruction ◽  
Reflectivity Data ◽  
Pulse Echo

Three-dimensional backprojection for reconstructing acoustic reflectivity within a volume is examined. The reflectivity data are acquired by means of a spherical array of point sources-receivers which encloses the object under study. Reconstruction of the image is obtained by back-projecting the recorded pulse-echo data over spherical surfaces in image space. An analytical expression for the point spread function (PSF) generated by the backprojection process has been derived. This expression was evaluated for several different choices of the acoustic pulse: a narrowband pulse, wideband pulse, and two analytically-derived optimum pulses which provide the best sidelobe response and a mainlobe width equal to approximately 0.4Λc, where Λc is the wavelength corresponding to the upper cutoff frequency of the pulse. Excellent agreement was obtained between the theoretical PSF's for the different pulses and those obtained by computer simulation. A number of potential advantages of direct three-dimensional reconstruction relative to two-dimensional tomographic techniques are discussed, including (1) high resolution in three dimensions (2) the possibility of incorporating refraction effects in the reconstruction process (3) reduced sensitivity to limited viewing anglesand (4) improved signal-to-noise ratio (thus minimizing requirements for data redundancy).

Experimental and Theoretical Analysis of the Flow in a Centrifugal Compressor Volute

1993 ◽  
Vol 115 (3) ◽  
pp. 582-589 ◽  
Author(s):  
E. Ayder ◽  
R. Van den Braembussche ◽  
J. J. Brasz
Keyword(s):  
Centrifugal Compressor ◽  
Cross Sections ◽  
Swirling Flow ◽  
Three Dimensional ◽  
Elliptical Cross ◽  
Loss Model ◽  
Tangential Flow ◽  
Static Pressure Distribution ◽  
Flow Loss ◽  
Mean Streamline Analysis

Detailed measurements of the swirling flow in a centrifugal compressor volute with elliptical cross section are presented. They show important variations of the swirl and throughflow velocity, total and static pressure distribution at the different volute cross sections and at the diffuser exit. The basic mechanisms defining the complex three dimensional flow structure are clarified. The different sources of pressure loss have been investigated and used to improve the prediction capability of one-dimensional mean streamline analysis correlations. The tangential flow loss model under decelerating flow conditions and the friction loss model are confirmed. New empirical loss coefficients are proposed for the exit cone loss model and the tangential flow loss model for the case of accelerating flow in the volute.

Computer-Aided Three-Dimensional Reconstruction and Measurement of the Vestibular End-Organs

1988 ◽  
Vol 98 (3) ◽  
pp. 195-202 ◽  
Author(s):  
Akira Takagi ◽  
Isamu Sando ◽  
Akira Takagi ◽  
Isamu Sando
Keyword(s):  
Temporal Bone ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Small Computer ◽  
Lateral Semicircular Canal ◽  
3 Dimensional ◽  
Dimensional Reconstruction ◽  
Vestibular Endorgans ◽  
Length And Area ◽  
Bone Structures

It is very valuable for temporal bone morphologists to be able to recognize temporal bone serial sections in three dimensions and to be able to measure temporal bone structures three-dimensionally. We can now do 3-dimensional reconstruction to visualize the structures of vestibular endorgans (utricular and saccular maculae) and measure these endorgans in space by means of a small computer system and software that we developed. As well as obtaining the dimensions—such as length and area—of the utricular and saccular maculae, we also found that (1) most of the utricular macula lies in one plane, which is the same as the plane of the lateral semicircular canal, (2) the saccular macula is shaped like part of a sphere, and (3) the angle between the two maculae is less than a right angle. Such knowledge is indispensable to the evaluation of the function of the utricular and saccular maculae.)

scholarly journals Electron crystallography: imaging and single-crystal diffraction from powders

2007 ◽  
Vol 64 (1) ◽  
pp. 149-160 ◽  
Author(s):  
Xiaodong Zou ◽  
Sven Hovmöller
Keyword(s):  
Three Dimensional ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Crystallographic Structure ◽  
X Ray Diffraction ◽  
Electron Crystallography ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction ◽  
Recent Developments

The study of crystals at atomic level by electrons – electron crystallography – is an important complement to X-ray crystallography. There are two main advantages of structure determinations by electron crystallography compared to X-ray diffraction: (i) crystals millions of times smaller than those needed for X-ray diffraction can be studied and (ii) the phases of the crystallographic structure factors, which are lost in X-ray diffraction, are present in transmission-electron-microscopy (TEM) images. In this paper, some recent developments of electron crystallography and its applications, mainly on inorganic crystals, are shown. Crystal structures can be solved to atomic resolution in two dimensions as well as in three dimensions from both TEM images and electron diffraction. Different techniques developed for electron crystallography, including three-dimensional reconstruction, the electron precession technique and ultrafast electron crystallography, are reviewed. Examples of electron-crystallography applications are given. There is in principle no limitation to the complexity of the structures that can be solved by electron crystallography.

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