scholarly journals SEM-microphotogrammetry, a new take on an old method for generating high-resolution 3D models from SEM images

2017 ◽  
Vol 267 (2) ◽  
pp. 214-226 ◽  
Author(s):  
A.D. BALL ◽  
P.A. JOB ◽  
A.E.L. WALKER
Keyword(s):  
High Resolution ◽  
3D Models ◽  
Sem Images

scholarly journals Tracking late Pleistocene Neandertals on the Iberian coast

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Eduardo Mayoral ◽  
Ignacio Díaz-Martínez ◽  
Jéremy Duveau ◽  
Ana Santos ◽  
Antonio Rodríguez Ramírez ◽  
...  
Keyword(s):  
High Resolution ◽  
Iberian Peninsula ◽  
Social Group ◽  
Microbial Mats ◽  
3D Models ◽  
Age Classes ◽  
Upper Pleistocene ◽  
Wide Range ◽  
The World ◽  
Flooded Area

AbstractHere, we report the recent discovery of 87 Neandertal footprints on the Southwest of the Iberian Peninsula (Doñana shoreline, Spain) located on an upper Pleistocene aeolian littoral setting (about 106 ± 19 kyr). Morphometric comparisons, high resolution digital photogrammetric 3D models and detailed sedimentary analysis have been provided to characterized the footprints and the palaeoenvironment. The footprints were impressed in the shoreline of a hypersaline swamped area related to benthic microbial mats, close to the coastline. They have a rounded heel, a longitudinal arch, relatively short toes, and adducted hallux, and represent the oldest upper Pleistocene record of Neandertal footprints in the world. Among these 87 footprints, 31 are longitudinally complete and measure from 14 to 29 cm. The calculated statures range from 104 to 188 cm, with half of the data between 130 and 150 cm. The wide range of sizes of the footprints suggests the existence of a social group integrated by individuals of different age classes but dominated, however, by non-adult individuals. The footprints, which are outside the flooded area are oriented perpendicular to the shoreline. These 87 footprints reinforce the ecological scenario of Neandertal groups established in coastal areas.

scholarly journals High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qiu Sun ◽  
Alan Perez-Rathke ◽  
Daniel M. Czajkowsky ◽  
Zhifeng Shao ◽  
Jie Liang
Keyword(s):  
High Resolution ◽  
Single Cell ◽  
3D Models ◽  
Computational Method ◽  
Midblastula Transition ◽  
Genome Wide ◽  
Large Ensembles ◽  
Chromatin Folding ◽  
Function Relationship ◽  
Relationship Of

AbstractSingle-cell chromatin studies provide insights into how chromatin structure relates to functions of individual cells. However, balancing high-resolution and genome wide-coverage remains challenging. We describe a computational method for the reconstruction of large 3D-ensembles of single-cell (sc) chromatin conformations from population Hi-C that we apply to study embryogenesis in Drosophila. With minimal assumptions of physical properties and without adjustable parameters, our method generates large ensembles of chromatin conformations via deep-sampling. Our method identifies specific interactions, which constitute 5–6% of Hi-C frequencies, but surprisingly are sufficient to drive chromatin folding, giving rise to the observed Hi-C patterns. Modeled sc-chromatins quantify chromatin heterogeneity, revealing significant changes during embryogenesis. Furthermore, >50% of modeled sc-chromatin maintain topologically associating domains (TADs) in early embryos, when no population TADs are perceptible. Domain boundaries become fixated during development, with strong preference at binding-sites of insulator-complexes upon the midblastula transition. Overall, high-resolution 3D-ensembles of sc-chromatin conformations enable further in-depth interpretation of population Hi-C, improving understanding of the structure-function relationship of genome organization.

3D genome structure reconstruction from chromosomal contact data

2017 ◽  
Author(s):  
◽  
Tuan Anh Trieu
Keyword(s):  
High Resolution ◽  
Genome Structure ◽  
Cell Types ◽  
3D Models ◽  
Graphic User Interface ◽  
Soft Constraints ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Manual Adjustment ◽  
The Relationship

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Different cell types of an organism have the same DNA sequence, but they can function differently because their difference in 3D organization allows them to express different genes and has different cellular functions. Understanding the 3D organization of the genome is the key to understand functions of the cell. Chromosome conformation capture techniques like Hi-C and TCC that can capture interactions between proximal chromosome fragments have allowed the study of 3D genome organization in high resolution and high through-put. My work focuses on developing computational methods to reconstruct 3D genome structures from Hi-C data. I presented three methods to reconstruct 3D genome and chromosome structures. The first method can build 3D genome models from soft constraints of contacts and non-contacts. This method utilizes the concept of contact and non-contact to reconstruct 3D models without translating interaction frequencies into physical distances. The translation is commonly used by other methods even though it makes a strong assumption about the relationship between interaction frequencies and physical distances. In synthetic dataset, when the relationship was known, my method performed comparably with other methods assuming the relationship. This shows the potential of my method for real Hi-C datasets where the relationship is unknown. The limitation of the method is that it has parameters requiring manual adjustment. I developed the second method to reconstruct 3D genome models. This method utilizes a commonly used function to translate interaction frequencies to physical distances to build 3D models. I proposed a novel way to derive soft constraints to handle inconsistency in the data and to make the method robust. Building 3D models at high resolution is a more challenging problem as the number of constraints is small and the feasible space is larger. I introduced a third method to build 3D chromosome models at high resolution. The method reconstructs models at low resolution and then uses them to guide the reconstruction of models at high resolution. The last part of my work is the development of a comprehensive tool with intuitive graphic user interface to analyze Hi-C data, reconstruct and analyze 3D models.

Unmanned Aerial Vehicle (UAV) time-lapse monitoring of the instability processes affecting Varano Hill: A case study of the ancient Roman site of Villa Arianna

2021 ◽  
Author(s):  
Renato Somma ◽  
Alfredo Trocciola ◽  
Daniele Spizzichino ◽  
Alessandro Fedele ◽  
Gabriele Leoni ◽  
...  
Keyword(s):  
High Resolution ◽  
Spatial Data ◽  
Morphological Evolution ◽  
Archaeological Site ◽  
Pilot Project ◽  
Time Lapse ◽  
3D Models ◽  
Slope Instability ◽  
Test Case ◽  
Slope Instabilities

<p>The archaeological site of Villa Arianna - located on Varano Hill, south of Vesuvius - offer tantalizing information regarding first-century AD resilience to hydrogeological risk. Additionally, the site provides an important test case for mitigation efforts of current and future geo-hazard. Villa Arianna, notable in particular for its wall frescoes, is part of a complex of Roman villas built between 89 BC and AD 79 in the ancient coastal resort area of Stabiae. This villa complex is located on a morphological terrace that separates the ruins from the present-day urban center of Castellammare di Stabia. The Varano hill is formed of alternating pyroclastic deposits, from the Vesuvius Complex, and alluvial sediments, from the Sarno River. The area, in AD 79, was completely covered by PDCs from the Plinian eruption of Vesuvius. Due to the geomorphological structure the slope is prone to slope instability phenomena that are mainly represented by earth and debris flows, usually triggered by heavy rainfall. The susceptibility is worsened by changes in hydraulic and land-use conditions mainly caused by lack of maintenance of mitigation works. Villa Arianna is the subject of a joint pilot project of the INGV-ENEA-ISPRA that includes non-invasive monitoring techniques such as the use of UAVs to study the areas of the slope at higher risk of instability. The project, in particular, seeks to implement innovative mitigation solutions that are non-destructive to the cultural heritage. UAVs represent the fastest way to produce high-resolution 3D models of large sites and allow archaeologists to collect accurate spatial data that can be used for 3D GIS analyses. Through this pilot project, we have used detailed 3D models and high-resolution ortho-images for new analyses and documentation of the site and to map the slope instabilities that threatens the Villa Arianna site. Through multi-temporal analyses of different data acquisitions, we intend to define the detailed morphological evolution of the entire Varano slope. These analyses will allow us to highlight priority areas for future low-impact mitigation interventions.</p>

scholarly journals Evaluation of the Apple iPhone 12 Pro LiDAR for an Application in Geosciences

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gregor Luetzenburg ◽  
Aart Kroon ◽  
Anders A. Bjørk
Keyword(s):  
High Resolution ◽  
Optical Sensors ◽  
Cost Effective ◽  
Point Clouds ◽  
3D Models ◽  
Absolute Accuracy ◽  
Wide Range ◽  
Financial Investments ◽  
Coastal Cliff ◽  
High Resolution Models

AbstractTraditionally, topographic surveying in earth sciences requires high financial investments, elaborate logistics, complicated training of staff and extensive data processing. Recently, off-the-shelf drones with optical sensors already reduced the costs for obtaining a high-resolution dataset of an Earth surface considerably. Nevertheless, costs and complexity associated with topographic surveying are still high. In 2020, Apple Inc. released the iPad Pro 2020 and the iPhone 12 Pro with novel build-in LiDAR sensors. Here we investigate the basic technical capabilities of the LiDAR sensors and we test the application at a coastal cliff in Denmark. The results are compared to state-of-the-art Structure from Motion Multi-View Stereo (SfM MVS) point clouds. The LiDAR sensors create accurate high-resolution models of small objects with a side length > 10 cm with an absolute accuracy of ± 1 cm. 3D models with the dimensions of up to 130 × 15 × 10 m of a coastal cliff with an absolute accuracy of ± 10 cm are compiled. Overall, the versatility in handling outweighs the range limitations, making the Apple LiDAR devices cost-effective alternatives to established techniques in remote sensing with possible fields of application for a wide range of geo-scientific areas and teaching.

scholarly journals All Our Eggs In One Basket: Challenges of High Resolution X-Ray Micro-Computed Tomography of Great Auk Pinguinus impennis Eggshell

2018 ◽  
Vol 2 ◽  
pp. e25794
Author(s):  
Douglas Russell ◽  
Arianna Bernucci ◽  
Amy Scott-Murray ◽  
Duncan Jackson ◽  
Farah Ahmed ◽  
...  
Keyword(s):  
Computed Tomography ◽  
High Resolution ◽  
Structured Light ◽  
3D Models ◽  
Breeding Ecology ◽  
Micro Computed Tomography ◽  
History Museum ◽  
X Ray ◽  
X Ray Imaging ◽  
Scan Data

High resolution X-ray micro-computed tomography gives the ability to research objects in unprecedented detail in 3D without damaging them but applying these new techniques to specimens can be complex. In 2017 the Natural History Museum (NHM), London embarked on a ground-breaking project with University of Sheffield to compare extinct Great Auk Pinguinus impennis eggshell microstructure to that of their extant relatives to gain new insight into their breeding ecology. NHM has a ZEISS Xradia 520 Versa X-ray microscope capable of submicron X-ray imaging in 3D but using it required supporting and moving complete eggshells within the confined, potentially harsh, mechanised environment of the microscope without risk. Ensuring the correct position and orientation of each egg to image nine distinct areas on the eggshell was also a challenge. Collaboration with colleagues in the NHM Conservation and Imaging & Analysis Centres developed a bespoke solution to hold and protect the eggs during scanning. All six NHM Great Auk eggshells and the inside of the microscope were surface scanned using a handheld structured light scanner. Scan data produced 3D models from which accurate 3D printed plastic replicas were made of the three Great Auk eggs prioritised for research. Each replica was used to mould a two-part, custom-built, case for each egg constructed from conservation grade epoxy putty and lined with polyethylene foam. This provided close-fitting, durable cases which could be used for the 6-month duration of the project. Each case enclosed its matching Great Auk egg entirely and had the advantage of being rock-hard, electrically insulating and water, heat and chemical resistant. A system of three, interchangeable, tailor-made mounting brackets were designed that married with the cases and held them safely and precisely inside the microscope at the correct angles and positions for imaging. The structured light scan of the inside of the microscope was used to model the necessary rotational movements of the cases and brackets inside the scanner, ensuring that all movements had sufficient clearance to avoid risk of impact. This system successfully protected the fragile c. 200 year old eggs throughout 70 scanning sessions. This provides a methodology for high resolution X-ray micro-computed tomography imaging of any similarly sized, fragile, object.

A 3D Optimized Frequency–Wavenumber (FK), Time–Space Optimized Symplectic (TSOS) Hybrid Method for Teleseismic Wave Modeling

2021 ◽  
Author(s):  
Weijuan Meng ◽  
Dinghui Yang ◽  
Xingpeng Dong ◽  
Jian Ma
Keyword(s):  
High Resolution ◽  
Seismic Wave ◽  
Hybrid Method ◽  
High Efficiency ◽  
Reference Model ◽  
3D Models ◽  
Realistic Model ◽  
High Accuracy ◽  
Memory Requirement ◽  
Time Space

ABSTRACT Although teleseismic waveform tomography can provide high-resolution images of the deep mantle, it is still unrealistic to numerically simulate the whole domain of seismic wave propagation due to the huge amount of computation. In this article, we develop a new three-dimensional hybrid method to address this issue, which couples the modified frequency–wavenumber (FK) method with the 3D time–space optimized symplectic (TSOS) method. First, the FK method, which is used to calculate the semianalytical incident wavefields in the layered reference model, is modified to compute the wavefields efficiently with a significantly low-memory requirement. Second, 3D TSOS method is developed to model the seismic wave propagating in the local 3D heterogeneous domain. The low memory requirement of the modified FK method and the high accuracy of the TSOS method make it feasible to obtain highly accurate synthetic seismograms efficiently. A crust–upper mantle model for P-, SV-, and SH-wave incidences is calculated to benchmark the accuracy and efficiency of the 3D optimized FK-TSOS method. Numerical experiments for 3D models with heterogeneities, undulated discontinuous interfaces, and realistic model in eastern Tibet, illustrate the capability of hybrid method to accurately capture the scattered waves caused by heterogeneities in 3D medium. The 3D optimized FK-TSOS method developed shows low-memory requirement, high accuracy, and high efficiency, which makes it be a promising forward method to further apply to high-resolution mantle structure images beneath seismic array.

scholarly journals A Practical Methodology for Generating High-Resolution 3D Models of Open-Pit Slopes Using UAVs: Flight Path Planning and Optimization

2020 ◽  
Vol 12 (14) ◽  
pp. 2283
Author(s):  
Rushikesh Battulwar ◽  
Garrett Winkelmaier ◽  
Jorge Valencia ◽  
Masoud Zare Naghadehi ◽  
Bijan Peik ◽  
...  
Keyword(s):  
Genetic Algorithm ◽  
High Resolution ◽  
Power Consumption ◽  
Fitness Function ◽  
Empirical Studies ◽  
3D Models ◽  
Open Pit ◽  
High Resolution Imagery ◽  
High Resolution Images ◽  
Using Data

High-resolution terrain models of open-pit mine highwalls and benches are essential in developing new automated slope monitoring systems for operational optimization. This paper presents several contributions to the field of remote sensing in surface mines providing a practical framework for generating high-resolution images using low-trim Unmanned Aerial Vehicles (UAVs). First, a novel mobile application was developed for autonomous drone flights to follow mine terrain and capture high-resolution images of the mine surface. In this article, case study is presented showcasing the ability of developed software to import area terrain, plan the flight accordingly, and finally execute the area mapping mission autonomously. Next, to model the drone’s battery performance, empirical studies were conducted considering various flight scenarios. A multivariate linear regression model for drone power consumption was derived from experimental data. The model has also been validated using data from a test flight. Finally, a genetic algorithm for solving the problem of flight planning and optimization has been employed. The developed power consumption model was used as the fitness function in the genetic algorithm. The designed algorithm was then validated using simulation studies. It is shown that the offered path optimization can reduce the time and energy of high-resolution imagery missions by over 50%. The current work provides a practical framework for stability monitoring of open-pit highwalls while achieving required energy optimization and imagery performance.

Digital Image Acquisition and Presentation for High Resolution SEM

1998 ◽  
Vol 4 (S2) ◽  
pp. 68-69
Author(s):  
Ya Chen
Keyword(s):  
High Resolution ◽  
Dwell Time ◽  
Signal To Noise Ratio ◽  
Image Acquisition ◽  
Incident Beam ◽  
Beam Intensity ◽  
Acquisition Time ◽  
Sem Images ◽  
Incident Beam Intensity ◽  
Image Averaging

Images obtained from an analog SEM are traditionally viewed and recorded from a cathode-ray tube (CRT). Many laboratories use instant film (e.g. Polaroid #52, #55 instant film) to justify image quality and obtain permanent image quickly. Digital imaging provides an alternative approach for image acquisition and recording. One major advantage of digital SEM is image averaging that allows one to improve the signal-to-noise ratio (SNR) from a noisy quick-scan image to reduce charging. SEM signal yield is proportional to incident beam intensity, image acquisition time or duration of beam interaction with specimen (dwell time). The higher beam intensity, or longer the dwell time, the more signal generated. However, for high-resolution SEM imaging, the beam dose and dwell time are limited by drafting, radiation damage, and contamination. Therefore high-resolution biological SEM images invariably have poor SNR.

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