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.

3D reconstruction of the 50s ribosomal subunit of escherichia coli

1986 ◽  
Vol 44 ◽  
pp. 40-41
Author(s):  
M. Radermacher ◽  
T. Wagenknecht ◽  
A. Verschoor ◽  
J. Frank
Keyword(s):  
3D Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
Ribosomal Subunit ◽  
Main Body ◽  
Large Ribosomal Subunit ◽  
E Coli ◽  
Reconstruction Scheme ◽  
Particle Preparation ◽  
Electron Microscopical

The three-dimensional (3D) structure of the large ribosomal subunit from E. coli was determined from micrographs of a negatively stained 50S particle preparation using our new reconstruction scheme. The 50S subunit occurs in electron microscopical preparations mainly in the crown-view orientation with the interface side of the main body situated parallel to the specimen plane, but in random in plane orientations. An image of such a specimen tilted by a large tilt angle, which inherently contains a conical tilt series of the particle, was used to calculate a 3D reconstruction.

A Self-Supervised Learning Technique for Road Defects Detection Based on Monocular Three-Dimensional Reconstruction

2019 ◽  
Author(s):  
Yazhe Hu ◽  
Tomonari Furukawa
Keyword(s):  
3D Reconstruction ◽  
Supervised Learning ◽  
Surface Defects ◽  
Three Dimensional ◽  
Road Surface ◽  
Class Prediction ◽  
Reconstruction Process ◽  
Learning Technique ◽  
Dimensional Reconstruction ◽  
Network Output

Abstract This paper presents a self-supervised learning technique for road surface defects detection using a monocular camera. The uniqueness of the proposed technique relies on its self-supervised learning structure which is achieved by combining physics-driven three-dimensional (3D) reconstruction with data-driven Convolutional Neural Network (CNN). Only images from one camera are needed as the inputs to the model without human labeling. The 3D point cloud are reconstructed from input images based on a near-planar road 3D reconstruction process to self-supervise the learning process. During testing, the network receives images and predicts the images as defect or non-defect. A refined class prediction is produced by combining the 3D road surface data with the network output when the belief of original network prediction is not strong enough to conclude the classification. Experiments are conducted on real road surface images to find the optimal parameters for this model. The testing results demonstrate the robustness and effectiveness of the proposed self-supervised road surface defects detection technique.

scholarly journals The Roman pier of San Cataldo: from archaeological data to 3D reconstruction

2019 ◽  
Vol 10 (20) ◽  
pp. 28 ◽  
Author(s):  
Ivan Ferrari ◽  
Aurora Quarta
Keyword(s):  
3D Reconstruction ◽  
Three Dimensional ◽  
Reconstruction Process ◽  
Aerial Photos ◽  
Archaeological Data ◽  
Production Pipeline ◽  
Starting Point ◽  
Adriatic Coast ◽  
Surrounding Landscape ◽  
Roman Age

<p>The pier of San Cataldo (Lecce, Italy) is located along the Adriatic coast about 10 km east-northeast of the ancient city of Lupiae, (today's Lecce), and is the best-preserved port structure of the Roman Age in Apulia. It was researched between 2004 and 2007 by the Laboratory of Topography and Photogrammetry (LabTAF) of the University of Salento, who produced a detailed analysis of the remain and a survey of the portion still visible on the mainland. At the same time, aerial surveys and the study of historic aerial photos from the 1940s and 50s supported a topographic study of the site. Since 2013, within the activities of the LabTAF, the structure has been the subject of an excavation campaign where a further portion of the pier was discovered in the mainland, and the underwater remains were documented. This contribution aims to emphasise the importance of collecting complete metric and historical-archaeological data for a proper three-dimensional (3D) reconstruction of the structure. On this occasion a photogrammetric survey was conducted and a 3D image-based model created that has become the starting point of the reconstruction hypothesis of the pier and its topographical context. The final model represents a reasonable synthesis of the interpretation of the collected data, and serves as a starting point for tackling the future integration or modification of the structure.</p><p><strong>Highlights:</strong></p><ul><li><p>A key requirement for a better understanding of the Roman pier of San Cataldo (Lecce, Italy) was the creation of a 3D model from an image-based survey.</p></li><li><p>The 3D reconstruction process of the monument was based on a production pipeline anchored to metric data and historical-archaeological information.</p></li><li><p>The final 3D reconstruction proposal shows the original shape of the Roman pier, the ancient surrounding landscape and its related activities.</p></li></ul>

scholarly journals Degenerate Near-Planar 3D Reconstruction from Two Overlapped Images for Road Defects Detection

Sensors ◽  
2020 ◽  
Vol 20 (6) ◽  
pp. 1640
Author(s):  
Yazhe Hu ◽  
Tomonari Furukawa
Keyword(s):  
3D Reconstruction ◽  
Surface Defects ◽  
Three Dimensional ◽  
Recall Rate ◽  
Reconstruction Error ◽  
Vertical Movement ◽  
Road Surface ◽  
Reconstruction Process ◽  
The Road ◽  
Road Surfaces

This paper presents a technique to reconstruct a three-dimensional (3D) road surface from two overlapped images for road defects detection using a downward-facing camera. Since some road defects, such as potholes, are characterized by 3D geometry, the proposed technique reconstructs road surfaces from the overlapped images prior to defect detection. The uniqueness of the proposed technique lies in the use of near-planar characteristics of road surfaces‘ in the 3D reconstruction process, which solves the degenerate road surface reconstruction problem. The reconstructed road surfaces thus result from the richer information. Therefore, the proposed technique detects road surface defects based on the accuracy-enhanced 3D reconstruction. Parametric studies were first performed in a simulated environment to analyze the 3D reconstruction error affected by different variables and show that the reconstruction errors caused by the camera’s image noise, orientation, and vertical movement are so small that they do not affect the road defects detection. Detailed accuracy analysis then shows that the mean and standard deviation of the errors are less than 0.6 mm and 1 mm through real road surface images. Finally, on-road tests demonstrate the effectiveness of the proposed technique in identifying road defects while having over 94% in precision, accuracy, and recall rate.

scholarly journals Highly tunable properties in pressure-treated two-dimensional Dion–Jacobson perovskites

2020 ◽  
Vol 117 (28) ◽  
pp. 16121-16126 ◽  
Author(s):  
Lingping Kong ◽  
Gang Liu ◽  
Jue Gong ◽  
Lingling Mao ◽  
Mengting Chen ◽  
...  
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Strain Engineering ◽  
Ex Situ ◽  
Light Absorber ◽  
Absorber Material ◽  
Order Of Magnitude ◽  
Condensed Matters ◽  
Novel Structures

The application of pressure can achieve novel structures and exotic phenomena in condensed matters. However, such pressure-induced transformations are generally reversible and useless for engineering materials for ambient-environment applications. Here, we report comprehensive high-pressure investigations on a series of Dion–Jacobson (D-J) perovskites A′An−1PbnI3n+1[A′ = 3-(aminomethyl) piperidinium (3AMP), A = methylammonium (MA),n= 1, 2, 4]. Our study demonstrates their irreversible behavior, which suggests pressure/strain engineering could viably improve light-absorber material not only in situ but also ex situ, thus potentially fostering the development of optoelectronic and electroluminescent materials. We discovered that the photoluminescence (PL) intensities are remarkably enhanced by one order of magnitude at mild pressures. Also, higher pressure significantly changes the lattices, boundary conditions of electronic wave functions, and possibly leads to semiconductor–metal transitions. For (3AMP)(MA)3Pb4I13, permanent recrystallization from 2D to three-dimensional (3D) structure occurs upon decompression, with dramatic changes in optical properties.

Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution

2018 ◽  
Vol 25 (4) ◽  
pp. 1010-1021 ◽  
Author(s):  
Miki Nakano ◽  
Osamu Miyashita ◽  
Slavica Jonic ◽  
Atsushi Tokuhisa ◽  
Florence Tama
Keyword(s):  
3D Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
3D Models ◽  
Molecular Structures ◽  
Experimental Conditions ◽  
Beam Incidence ◽  
Minimum Requirements ◽  
Diffraction Patterns ◽  
Insight Into

Three-dimensional (3D) structures of biomolecules provide insight into their functions. Using X-ray free-electron laser (XFEL) scattering experiments, it was possible to observe biomolecules that are difficult to crystallize, under conditions that are similar to their natural environment. However, resolving 3D structure from XFEL data is not without its challenges. For example, strong beam intensity is required to obtain sufficient diffraction signal and the beam incidence angles to the molecule need to be estimated for diffraction patterns with significant noise. Therefore, it is important to quantitatively assess how the experimental conditions such as the amount of data and their quality affect the expected resolution of the resulting 3D models. In this study, as an example, the restoration of 3D structure of ribosome from two-dimensional diffraction patterns created by simulation is shown. Tests are performed using the diffraction patterns simulated for different beam intensities and using different numbers of these patterns. Guidelines for selecting parameters for slice-matching 3D reconstruction procedures are established. Also, the minimum requirements for XFEL experimental conditions to obtain diffraction patterns for reconstructing molecular structures to a high-resolution of a few nanometers are discussed.

scholarly journals 3D Reconstruction Based on Fusing Active Structured Laser and Passive Stereo Techniques

2020 ◽  
Vol 23 (3) ◽  
pp. 277-288
Author(s):  
Shahad A. Al-Saqal ◽  
Ali A. Al-Temeemy
Keyword(s):  
3D Reconstruction ◽  
Laser Scanning ◽  
Three Dimensional ◽  
Scanning System ◽  
Fusion Method ◽  
Reconstruction Process ◽  
Reconstruction Performance ◽  
Dimensional Reconstruction ◽  
Real Objects ◽  
Laser Scanning System

Three-dimensional reconstruction of real objects comprises capturing the appearance and the shape for these objects and determining the three-dimensional coordinates for their profiles. This reconstruction process can be accomplished either by using active or passive techniques. In this paper, a new fusion method is proposed for 3D reconstruction. This method exploits the advantages of both stereo-based passive and laser-based active techniques and overcomes their limitations to improve the performance of 3D reconstruction. With this method, a hybrid laser-based structured light scanning system is designed and implemented. This system captures the required information using passive and active techniques and uses the proposed fusion method for 3D reconstruction. The performance of the proposed method and its scanning system were experimentally evaluated. The evaluation results show high reconstruction performance for the proposed fusion method over the traditional 3D reconstruction techniques. The results also show the effectiveness of the hybrid laser scanning system and its ability to scan and reconstruct the shape and the appearance for real objects using the proposed fusion method.

scholarly journals REKONTRUKSI MODEL 3D DARI BANYAK GAMBAR MENGGUNAKAN ALGORITMA STRUCTURE FROM MOTION (SFM) DAN MULTI VIEW STEREO (MVS) BERBASIS COMPUTER VISION

2020 ◽  
Vol 3 (2) ◽  
pp. 108-113
Author(s):  
Moch.d Kholil ◽  
Ismanto Ismanto ◽  
M. Nur Fu’ad
Keyword(s):  
3D Reconstruction ◽  
3D Modeling ◽  
Structure From Motion ◽  
3D Model ◽  
Three Dimensional ◽  
Original Image ◽  
Architecture Education ◽  
Reconstruction Process ◽  
3D Objects ◽  
3D Model Reconstruction

With the development of the field of Information and Computer Technology (ICT), three-dimensional technology (3D) is also growing rapidly. Currently, the need to visualize 3D objects is widely used in animation and graphics applications, architecture, education, cultural recognition and virtual reality. 3D modeling of historical buildings has become a concern in recent years. 3D reconstruction is a documentation effort for reconstruction or restoration if the building is destroyed. By using a 3D model reconstruction approach based on multiple images using the Structure From Motion (SFM) and Multi View Stereo (MVS) algorithm, it is hoped that the 3D modeling results can be used as an effort to preserve 3D objects in the cultural heritage area of Penataran Temple. This research was conducted by taking an object in the form of photos as many as 61 pictures in the area of ​​the Blitar Penataran Temple. The resulting photos are reconstructed into a 3D model using the Structure From Motion algorithm in the meshroom. In this study, a test was carried out on the original image with the compressed image for reconstruction to be compared to the 3D reconstruction process from the two input data. From 61 images processed using the Structure Form Motion algorithm, 33 camera pose and 3D point data were obtained, both original and compressed images. For the number of iterations the compressed image is 1.4% less than the original image and takes 43.53% faster than the original image.  

Methods for three-dimensional reconstruction of cellular components within a thick section

1986 ◽  
Vol 44 ◽  
pp. 18-21
Author(s):  
J. Frank ◽  
B. F. McEwen ◽  
M. Radermacher ◽  
C. L. Rieder
Keyword(s):  
Tilt Angle ◽  
Tomographic Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
Thick Section ◽  
Three Dimensional Reconstruction ◽  
Axis Ratio ◽  
Dimensional Reconstruction ◽  
Cellular Components

The tomographic reconstruction from multiple projections of cellular components, within a thick section, offers a way of visualizing and quantifying their three-dimensional (3D) structure. However, asymmetric objects require as many views from the widest tilt range as possible; otherwise the reconstruction may be uninterpretable. Even if not for geometric obstructions, the increasing pathway of electrons, as the tilt angle is increased, poses the ultimate upper limitation to the projection range. With the maximum tilt angle being fixed, the only way to improve the faithfulness of the reconstruction is by changing the mode of the tilting from single-axis to conical; a point within the object projected with a tilt angle of 60° and a full 360° azimuthal range is then reconstructed as a slightly elliptic (axis ratio 1.2 : 1) sphere.

Cryomicroscopy of crotoxin complex crystals at 400 KV

1989 ◽  
Vol 47 ◽  
pp. 826-827
Author(s):  
Jaap Brink ◽  
Wah Chiu
Keyword(s):  
Signal To Noise Ratio ◽  
3D Structure ◽  
Three Dimensional ◽  
Carbon Films ◽  
Depth Of Field ◽  
Basic Subunit ◽  
Ewald Sphere ◽  
Diffraction Patterns ◽  
Complex Crystals ◽  
Acidic Subunit

The crotoxin complex is a potent neurotoxin composed of a basic subunit (Mr = 12,000) and an acidic subunit (M = 10,000). The basic subunit possesses phospholipase activity whereas the acidic subunit shows no enzymatic activity at all. The complex's toxocity is expressed both pre- and post-synaptically. The crotoxin complex forms thin crystals suitable for electron crystallography. The crystals diffract up to 0.16 nm in the microscope, whereas images show reflections out to 0.39 nm2. Ultimate goal in this study is to obtain a three-dimensional (3D-) structure map of the protein around 0.3 nm resolution. Use of 100 keV electrons in this is limited; the unit cell's height c of 25.6 nm causes problems associated with multiple scattering, radiation damage, limited depth of field and a more pronounced Ewald sphere curvature. In general, they lead to projections of the unit cell, which at the desired resolution, cannot be interpreted following the weak-phase approximation. Circumventing this problem is possible through the use of 400 keV electrons. Although the overall contrast is lowered due to a smaller scattering cross-section, the signal-to-noise ratio of especially higher order reflections will improve due to a smaller contribution of inelastic scattering. We report here our preliminary results demonstrating the feasability of the data collection procedure at 400 kV.Crystals of crotoxin complex were prepared on carbon-covered holey-carbon films, quench frozen in liquid ethane, inserted into a Gatan 626 holder, transferred into a JEOL 4000EX electron microscope equipped with a pair of anticontaminators operating at −184°C and examined under low-dose conditions. Selected area electron diffraction patterns (EDP's) and images of the crystals were recorded at 400 kV and −167°C with dose levels of 5 and 9.5 electrons/Å, respectively.

Sign in / Sign up

Export Citation Format

Share Document