Detection, Averaging, and 3D Reconstruction of Biological Specimens on Hypercubes (Transputer-based) Computers

1990 ◽  
Vol 48 (1) ◽  
pp. 454-455
Author(s):  
Jose-Maria Carazo ◽  
I. Benavides ◽  
S. Marco ◽  
J.L. Carrascosa ◽  
E.L. Zapata
Keyword(s):  
3D Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
Software Tools ◽  
Mapping Method ◽  
Computer Architectures ◽  
Parallel Computer ◽  
Reconstruction Process ◽  
Computing Power ◽  
Order Of Magnitude

Obtaining the three-dimensional (3D) structure of negatively stained biological specimens at a resolution of, typically, 2 - 4 nm is becoming a relatively common practice in an increasing number of laboratories. A combination of new conceptual approaches, new software tools, and faster computers have made this situation possible. However, all these 3D reconstruction processes are quite computer intensive, and the middle term future is full of suggestions entailing an even greater need of computing power. Up to now all published 3D reconstructions in this field have been performed on conventional (sequential) computers, but it is a fact that new parallel computer architectures represent the potential of order-of-magnitude increases in computing power and should, therefore, be considered for their possible application in the most computing intensive tasks.We have studied both shared-memory-based computer architectures, like the BBN Butterfly, and local-memory-based architectures, mainly hypercubes implemented on transputers, where we have used the algorithmic mapping method proposed by Zapata el at. In this work we have developed the basic software tools needed to obtain a 3D reconstruction from non-crystalline specimens (“single particles”) using the so-called Random Conical Tilt Series Method. We start from a pair of images presenting the same field, first tilted (by ≃55°) and then untilted. It is then assumed that we can supply the system with the image of the particle we are looking for (ideally, a 2D average from a previous study) and with a matrix describing the geometrical relationships between the tilted and untilted fields (this step is now accomplished by interactively marking a few pairs of corresponding features in the two fields). From here on the 3D reconstruction process may be run automatically.

Structural Studies on the Eukaryotic Ribosome

1990 ◽  
Vol 48 (1) ◽  
pp. 256-257
Author(s):  
Adriana Verschoor ◽  
Ronald Milligan ◽  
Suman Srivastava ◽  
Joachim Frank
Keyword(s):  
Chick Embryo ◽  
3D Reconstruction ◽  
Single Particle ◽  
Mass Density ◽  
Particle Surface ◽  
Uranyl Acetate ◽  
Electron Microscopic ◽  
Eukaryotic Ribosome ◽  
Negative Stain ◽  
Reconstruction Methods

We have studied the eukaryotic ribosome from two vertebrate species (rabbit reticulocyte and chick embryo ribosomes) in several different electron microscopic preparations (Fig. 1a-d), and we have applied image processing methods to two of the types of images. Reticulocyte ribosomes were examined in both negative stain (0.5% uranyl acetate, in a double-carbon preparation) and frozen hydrated preparation as single-particle specimens. In addition, chick embryo ribosomes in tetrameric and crystalline assemblies in frozen hydrated preparation have been examined. 2D averaging, multivariate statistical analysis, and classification methods have been applied to the negatively stained single-particle micrographs and the frozen hydrated tetramer micrographs to obtain statistically well defined projection images of the ribosome (Fig. 2a,c). 3D reconstruction methods, the random conical reconstruction scheme and weighted back projection, were applied to the negative-stain data, and several closely related reconstructions were obtained. The principal 3D reconstruction (Fig. 2b), which has a resolution of 3.7 nm according to the differential phase residual criterion, can be compared to the images of individual ribosomes in a 2D tetramer average (Fig. 2c) at a similar resolution, and a good agreement of the general morphology and of many of the characteristic features is seen.Both data sets show the ribosome in roughly the same ’view’ or orientation, with respect to the adsorptive surface in the electron microscopic preparation, as judged by the agreement in both the projected form and the distribution of characteristic density features. The negative-stain reconstruction reveals details of the ribosome morphology; the 2D frozen-hydrated average provides projection information on the native mass-density distribution within the structure. The 40S subunit appears to have an elongate core of higher density, while the 60S subunit shows a more complex pattern of dense features, comprising a rather globular core, locally extending close to the particle surface.

3D reconstruction and calculation of surface area and volume of bell pepper

2007 ◽  
Vol 3 (1) ◽  
pp. 89-113
Author(s):  
Zoltán Gillay ◽  
László Fenyvesi
Keyword(s):  
3D Reconstruction ◽  
Surface Area ◽  
Three Dimensional ◽  
Reference Method ◽  
Bell Pepper ◽  
Three Dimensional Model ◽  
Acceptable Error ◽  
Volume Calculation ◽  
Bell Peppers ◽  
Area And Volume

There was a method developed that generates the three-dimensional model of not axisymmetric produce, based on an arbitrary number of photos. The model can serve as a basis for calculating the surface area and the volume of produce. The efficiency of the reconstruction was tested on bell peppers and artificial shapes. In case of bell peppers 3-dimensional reconstruction was created from 4 images rotated in 45° angle intervals. The surface area and the volume were estimated on the basis of the reconstructed area. Furthermore, a new and simple reference method was devised to give precise results for the surface area of bell pepper. The results show that this 3D reconstruction-based surface area and volume calculation method is suitable to determine the surface area and volume of definite bell peppers with an acceptable error.

Three-dimensional Reconstruction of Microscopic Image Based on Multi-ST Algorithm

2020 ◽  
Vol 64 (2) ◽  
pp. 20506-1-20506-7
Author(s):  
Min Zhu ◽  
Rongfu Zhang ◽  
Pei Ma ◽  
Xuedian Zhang ◽  
Qi Guo
Keyword(s):  
3D Reconstruction ◽  
Three Dimensional ◽  
Scale Model ◽  
Microscopic Image ◽  
Multi Scale ◽  
Gaussian Pyramid ◽  
Cost Aggregation ◽  
Dimensional Reconstruction ◽  
Image Pairs ◽  
Accurate Matching

Abstract Three-dimensional (3D) reconstruction is extensively used in microscopic applications. Reducing excessive error points and achieving accurate matching of weak texture regions have been the classical challenges for 3D microscopic vision. A Multi-ST algorithm was proposed to improve matching accuracy. The process is performed in two main stages: scaled microscopic images and regularized cost aggregation. First, microscopic image pairs with different scales were extracted according to the Gaussian pyramid criterion. Second, a novel cost aggregation approach based on the regularized multi-scale model was implemented into all scales to obtain the final cost. To evaluate the performances of the proposed Multi-ST algorithm and compare different algorithms, seven groups of images from the Middlebury dataset and four groups of experimental images obtained by a binocular microscopic system were analyzed. Disparity maps and reconstruction maps generated by the proposed approach contained more information and fewer outliers or artifacts. Furthermore, 3D reconstruction of the plug gauges using the Multi-ST algorithm showed that the error was less than 0.025 mm.

No-Reference Image Quality Assessment Based on Multi-Order Gradients Statistics

2020 ◽  
Vol 64 (1) ◽  
pp. 10505-1-10505-16
Author(s):  
Yin Zhang ◽  
Xuehan Bai ◽  
Junhua Yan ◽  
Yongqi Xiao ◽  
C. R. Chatwin ◽  
...  
Keyword(s):  
Neural Network ◽  
Image Quality ◽  
Quality Assessment ◽  
Image Quality Assessment ◽  
Assessment Method ◽  
Image Distortion ◽  
Image Feature ◽  
Reference Image ◽  
Gradient Magnitude ◽  
Distortion Type

Abstract A new blind image quality assessment method called No-Reference Image Quality Assessment Based on Multi-Order Gradients Statistics is proposed, which is aimed at solving the problem that the existing no-reference image quality assessment methods cannot determine the type of image distortion and that the quality evaluation has poor robustness for different types of distortion. In this article, an 18-dimensional image feature vector is constructed from gradient magnitude features, relative gradient orientation features, and relative gradient magnitude features over two scales and three orders on the basis of the relationship between multi-order gradient statistics and the type and degree of image distortion. The feature matrix and distortion types of known distorted images are used to train an AdaBoost_BP neural network to determine the image distortion type; the feature matrix and subjective scores of known distorted images are used to train an AdaBoost_BP neural network to determine the image distortion degree. A series of comparative experiments were carried out using Laboratory of Image and Video Engineering (LIVE), LIVE Multiply Distorted Image Quality, Tampere Image, and Optics Remote Sensing Image databases. Experimental results show that the proposed method has high distortion type judgment accuracy and that the quality score shows good subjective consistency and robustness for all types of distortion. The performance of the proposed method is not constricted to a particular database, and the proposed method has high operational efficiency.

Embedded Gold Markers for Improved TEM/STEM Tomography Reconstruction

2008 ◽  
Author(s):  
Jian-Shing Luo ◽  
Chia-Chi Huang ◽  
Jeremy D. Russell
Keyword(s):  
3D Reconstruction ◽  
Feature Tracking ◽  
Semiconductor Device ◽  
Electron Tomography ◽  
Tracking Process ◽  
Carbon Coated ◽  
Novel Method ◽  
Tomography Reconstruction ◽  
Tilt Series ◽  
20 Nm

Abstract Electron tomography includes four main steps: tomography data acquisition, image processing, 3D reconstruction, and visualization. After acquisition, tilt-series alignments are performed. Two methods are used to align the tilt-series: cross-correlation and feature tracking. Normally, about 10-20 nm of fiducial markers, such as gold beads, are deposited onto one side of 100 mesh carbon-coated grids during the feature-tracking process. This paper presents a novel method for preparing electron tomography samples with gold beads inside to improve the feature tracking process and quality of 3D reconstruction. Results show that the novel electron tomography sample preparation method improves image alignment, which is essential for successful tomography in many contemporary semiconductor device structures.

CPU-GPU Rendering of CT Scan Images for Vertebra Reconstruction from CT Scan Images with a Calibration Policy

2020 ◽  
pp. 1-5
Author(s):  
Usman Khan ◽  
Usman Khan ◽  
AmanUllah Yasin ◽  
Imran Shafi ◽  
Muhammad Abid
Keyword(s):  
3D Reconstruction ◽  
Ct Scan ◽  
Surface Reconstruction ◽  
3D Visualization ◽  
Cervical Vertebra ◽  
Marching Cubes ◽  
Affine Transform ◽  
Visualization Techniques ◽  
Visualization Algorithms ◽  
Gpu Implementation

In this work GPU implementation of classic 3D visualization algorithms namely Marching Cubes and Raycasting has been carried for cervical vertebra using VTK libraries. A proposed framework has been introduced for efficient and duly calibrated 3D reconstruction using Dicom Affine transform and Python Mayavi framework to address the limitation of benchmark visualization techniques i.e. lack of calibration, surface reconstruction artifacts and latency.

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