Image Analysis to Quantify Coral Bleaching Using Greyscale Model  v1

2021 ◽  
Author(s):  
Rowan Mclachlan ◽  
Andrea G Grottoli
Keyword(s):  
Image Analysis ◽  
Ex Situ ◽  
Live Coral ◽  
Reference Standard ◽  
Color Analysis ◽  
Mean Intensity ◽  
Coral Colony ◽  
Colony Color ◽  
Highly Correlated

This protocol outlines a method of quantitatively measuring the degree of bleaching of a coral colony non-destructively in the field using image analysis. Previous studies have shown that mean intensity grey (MIG), also known as percent whiteness, is highly correlated with chlorophyll a and Symbiodiniaceae density (Chow et al. 2016, Amid et al. 2018), and therefore can be used to quantify the bleaching intensity of a coral colony. Color analysis can be done using digital photographs of live coral colonies either in situ (e.g., Maguire et al. 2003) or ex-situ in the lab (Amid et al. 2018; this protocol). Photographs must be taken prior to any preservation or processing of tissue, such as freezing, use of preservatives or fixatives, airbrushing etc., to ensure no alteration of the original coral color occurs. In this protocol, corals are photographed in front of a white reference standard and the resulting color images are subsequently converted to 8-bit greyscale and analyzed. There are two steps to this protocol: 1) Photographing live coral fragments 2) Image analysis of mean grey value This protocol was written by Dr. Rowan McLachlan and was reviewed by Dr. Andréa Grottoli. Acknowledgments I would like to thank Dr. Eugene Katrukha for kindly taking the time to teach me this method, and providing me feedback on how to produce higher quality images for analysis.

scholarly journals Tutupan Terumbu Karang pada Kedalaman Berbeda di Perairan Pantai Batu Sungu, Desa Les, Kabupaten Buleleng

2021 ◽  
Vol 4 (2) ◽  
pp. 42
Author(s):  
I Putu Dede Charles Dharma Saputra ◽  
IGB Sila Dharma ◽  
Yulianto Suteja ◽  
Widiastuti Widiastuti
Keyword(s):  
Water Quality ◽  
Coral Cover ◽  
Management Plan ◽  
Coral Growth ◽  
Ex Situ ◽  
Live Coral ◽  
Growth Forms ◽  
Significant Difference ◽  
Study Sites

Bali island has many magnificent underwater coral reef gardens that attract tourists. Besides Pemuteran and Menjangan island waters,  Batu Sungu water has also potential to be a new tourist destination. Thus, to determine the potency and management plan in Batu Sungu waters, this research aimed to examine the overall coral cover, coral growth forms, other benthic forms, and each of their components in 5 and 10 m depths.  The overall coral cover, coral growth forms, other benthic forms, and each of their components were counted by using the Line Intercept Transect (LIT) method. Before collecting data, study sites were observed by using the Manta Tow method. Data were collected in 2 depths (5 dan 10 m) with 5 sites each (replicates) that separates within 50 to 150 m. A 25 m LIT was spread parallel to the coastline above the reefs. Live coral colonies, other benthic forms below the transects were measured for the number, length, and growth forms. Water quality was measured in situ (temperature, current, and clarity) and ex situ (pH). Results showed that the category of coral coverage in Batu Sungu water is "good” in 5 m and "moderate” in 10 m whereas there was no significant difference among each component of the overall coral cover. The most dominant coral growth form among the 2 depths was Coral Massive whereas significantly abundant in 5 m. Moreover, the number of Coral Foliose was found significantly high in the same depth. Other coral growth forms were relatively similar in numbers in two depths.  As likewise, the cover of other benthic forms and its component were not significantly different among two depths, except  Dead Coral with Algae which significantly plentiful in 5 m. Sand was dominantly found in two depths with no significant difference. Furthermore, Coraline Alga was only observed in 5 m, however, there were no Macroalga and Alga Assemblages found at this depth. It is assumed that the similarity number of the overall coral cover, coral growth forms, other benthic forms, and each of their components is related to the alikeness of water quality among the two depths. 

An in situ and ex situ TEM study of the formation of thin cobalt silicide films by molecular beam epitaxy on the silicon (100) surface

1988 ◽  
Vol 46 ◽  
pp. 884-885
Author(s):  
D. Loretto ◽  
J. M. Gibson ◽  
S. M. Yalisove ◽  
R. T. Tung
Keyword(s):  
Molecular Beam Epitaxy ◽  
Molecular Beam ◽  
Defect Density ◽  
High Vacuum ◽  
Ultra High Vacuum ◽  
Ex Situ ◽  
Metal Base ◽  
In Situ Experiments ◽  
Potential Applications

The cobalt disilicide/silicon system has potential applications as a metal-base and as a permeable-base transistor. Although thin, low defect density, films of CoSi2 on Si(111) have been successfully grown, there are reasons to believe that Si(100)/CoSi2 may be better suited to the transmission of electrons at the silicon/silicide interface than Si(111)/CoSi2. A TEM study of the formation of CoSi2 on Si(100) is therefore being conducted. We have previously reported TEM observations on Si(111)/CoSi2 grown both in situ, in an ultra high vacuum (UHV) TEM and ex situ, in a conventional Molecular Beam Epitaxy system.The procedures used for the MBE growth have been described elsewhere. In situ experiments were performed in a JEOL 200CX electron microscope, extensively modified to give a vacuum of better than 10-9 T in the specimen region and the capacity to do in situ sample heating and deposition. Cobalt was deposited onto clean Si(100) samples by thermal evaporation from cobalt-coated Ta filaments.

The use of transmission and analytical electron microscopy in studying reactions and phase transformations in thin film

1993 ◽  
Vol 51 ◽  
pp. 842-843
Author(s):  
K. Barmak
Keyword(s):  
Thin Film ◽  
Thin Films ◽  
Phase Transformations ◽  
Analytical Electron Microscopy ◽  
Ex Situ ◽  
Multilayer Thin Films ◽  
Absolute Concentration ◽  
Analytical Electron ◽  
Deposition Step

Generally, processing of thin films involves several annealing steps in addition to the deposition step. During the annealing steps, diffusion, transformations and reactions take place. In this paper, examples of the use of TEM and AEM for ex situ and in situ studies of reactions and phase transformations in thin films will be presented.The ex situ studies were carried out on Nb/Al multilayer thin films annealed to different stages of reaction. Figure 1 shows a multilayer with dNb = 383 and dAl = 117 nm annealed at 750°C for 4 hours. As can be seen in the micrograph, there are four phases, Nb/Nb3-xAl/Nb2-xAl/NbAl3, present in the film at this stage of the reaction. The composition of each of the four regions marked 1-4 was obtained by EDX analysis. The absolute concentration in each region could not be determined due to the lack of thickness and geometry parameters that were required to make the necessary absorption and fluorescence corrections.

Transmission Electron Microscopy of Epitaxial silicides grown by ultra high vacuum deposition

1989 ◽  
Vol 47 ◽  
pp. 462-463
Author(s):  
D. Loretto ◽  
J. M. Gibson ◽  
S. M. Yalisove
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Electron Diffraction ◽  
High Vacuum ◽  
High Energy ◽  
Energy Electron ◽  
Ultra High Vacuum ◽  
Ex Situ ◽  
Transmission Electron

The silicides CoSi2 and NiSi2 are both metallic with the fee flourite structure and lattice constants which are close to silicon (1.2% and 0.6% smaller at room temperature respectively) Consequently epitaxial cobalt and nickel disilicide can be grown on silicon. If these layers are formed by ultra high vacuum (UHV) deposition (also known as molecular beam epitaxy or MBE) their thickness can be controlled to within a few monolayers. Such ultrathin metal/silicon systems have many potential applications: for example electronic devices based on ballistic transport. They also provide a model system to study the properties of heterointerfaces. In this work we will discuss results obtained using in situ and ex situ transmission electron microscopy (TEM).In situ TEM is suited to the study of MBE growth for several reasons. It offers high spatial resolution and the ability to penetrate many monolayers of material. This is in contrast to the techniques which are usually employed for in situ measurements in MBE, for example low energy electron diffraction (LEED) and reflection high energy electron diffraction (RHEED), which are both sensitive to only a few monolayers at the surface.

Atomic Layer Deposition of LiF and Lithium Ion Conducting (AlF3)(LiF)x Alloys Using Trimethylaluminum, Lithium Hexamethyldisilazide and Hydrogen Fluoride

2017 ◽  
Author(s):  
Younghee Lee ◽  
Daniela M. Piper ◽  
Andrew S. Cavanagh ◽  
Matthias J. Young ◽  
Se-Hee Lee ◽  
...  
Keyword(s):  
Lithium Ion ◽  
Atomic Layer ◽  
Mass Gain ◽  
Alloy Film ◽  
Ex Situ ◽  
X Ray ◽  
Layer Deposition ◽  
Ion Conducting ◽  
Good Agreement

<div>Atomic layer deposition (ALD) of LiF and lithium ion conducting (AlF<sub>3</sub>)(LiF)<sub>x</sub> alloys was developed using trimethylaluminum, lithium hexamethyldisilazide (LiHMDS) and hydrogen fluoride derived from HF-pyridine solution. ALD of LiF was studied using in situ quartz crystal microbalance (QCM) and in situ quadrupole mass spectrometer (QMS) at reaction temperatures between 125°C and 250°C. A mass gain per cycle of 12 ng/(cm<sup>2</sup> cycle) was obtained from QCM measurements at 150°C and decreased at higher temperatures. QMS detected FSi(CH<sub>3</sub>)<sub>3</sub> as a reaction byproduct instead of HMDS at 150°C. LiF ALD showed self-limiting behavior. Ex situ measurements using X-ray reflectivity (XRR) and spectroscopic ellipsometry (SE) showed a growth rate of 0.5-0.6 Å/cycle, in good agreement with the in situ QCM measurements.</div><div>ALD of lithium ion conducting (AlF3)(LiF)x alloys was also demonstrated using in situ QCM and in situ QMS at reaction temperatures at 150°C A mass gain per sequence of 22 ng/(cm<sup>2</sup> cycle) was obtained from QCM measurements at 150°C. Ex situ measurements using XRR and SE showed a linear growth rate of 0.9 Å/sequence, in good agreement with the in situ QCM measurements. Stoichiometry between AlF<sub>3</sub> and LiF by QCM experiment was calculated to 1:2.8. XPS showed LiF film consist of lithium and fluorine. XPS also showed (AlF<sub>3</sub>)(LiF)x alloy consists of aluminum, lithium and fluorine. Carbon, oxygen, and nitrogen impurities were both below the detection limit of XPS. Grazing incidence X-ray diffraction (GIXRD) observed that LiF and (AlF<sub>3</sub>)(LiF)<sub>x</sub> alloy film have crystalline structures. Inductively coupled plasma mass spectrometry (ICP-MS) and ionic chromatography revealed atomic ratio of Li:F=1:1.1 and Al:Li:F=1:2.7: 5.4 for (AlF<sub>3</sub>)(LiF)<sub>x</sub> alloy film. These atomic ratios were consistent with the calculation from QCM experiments. Finally, lithium ion conductivity (AlF<sub>3</sub>)(LiF)<sub>x</sub> alloy film was measured as σ = 7.5 × 10<sup>-6</sup> S/cm.</div>

A New Method of Wafer Level Plan View TEM Sample Preparation by DualBeam

2008 ◽  
Author(s):  
Hyoung H. Kang ◽  
Michael A. Gribelyuk ◽  
Oliver D. Patterson ◽  
Steven B. Herschbein ◽  
Corey Senowitz
Keyword(s):  
Sample Preparation ◽  
Ex Situ ◽  
Wafer Level ◽  
Cross Sectional ◽  
Plan View ◽  
Manufacturing Line ◽  
Transmission Electron ◽  
Thin Lamella ◽  
Preparation Techniques

Abstract Cross-sectional style transmission electron microscopy (TEM) sample preparation techniques by DualBeam (SEM/FIB) systems are widely used in both laboratory and manufacturing lines with either in-situ or ex-situ lift out methods. By contrast, however, the plan view TEM sample has only been prepared in the laboratory environment, and only after breaking the wafer. This paper introduces a novel methodology for in-line, plan view TEM sample preparation at the 300mm wafer level that does not require breaking the wafer. It also presents the benefit of the technique on electrically short defects. The methodology of thin lamella TEM sample preparation for plan view work in two different tool configurations is also presented. The detailed procedure of thin lamella sample preparation is also described. In-line, full wafer plan view (S)TEM provides a quick turn around solution for defect analysis in the manufacturing line.

PROPUESTA DE CONSERVACIÓN DE TRES ESPECIES MEXICANAS DE PICEA EN PELIGRO DE EXTINCIÓN

2015 ◽  
Vol 38 (3) ◽  
pp. 235 ◽  
Author(s):  
Eduardo Mendoza-Maya ◽  
Judith Espino-Espino ◽  
Carmen Z. Quiñones-Pérez ◽  
Celestino Flores-López ◽  
Christian Wehenkel ◽  
...  
Keyword(s):  
Ex Situ

Picea mexicana Martínez, P. chihuahuana Martínez y P. martinezii Patterson son especies endémicas de México en peligro de extinción. Se presenta una síntesis de su situación actual y una propuesta de manejo para su conservación in situ y ex situ, con base en la diversidad y estructura genética de las poblaciones y la ubicación de las áreas en donde se predice existirá el hábitat climático que les es propicio en el futuro (años 2030, 2060 y 2090; al promediar los modelos Canadiense, Hadley y Geofísica de Fluidos con escenarios de emisiones A y B). Para la conservación in situ se plantea la protección, el incremento de la diversidad genética y la expansión de las tres únicas poblaciones de P. mexicana, las cuatro únicas de P. martinezii y ocho poblaciones designadas prioritarias de las 40 poblaciones de P. chihuahuana, mediante la plantación de individuos originados de otras poblaciones hasta alcanzar un tamaño mínimo de población genéticamente viable (entre 1035 a 3836 individuos). Para la conservación ex situ se propone el establecimiento de poblaciones en sitios fuera del rango de distribución natural de las especies, en donde se ha proyectado que ocurrirá el clima que les es propicio, con al menos 3606 individuos de P. mexicana en el volcán Cofre de Perote, Veracruz; 2431 individuos de P. chihuahuana en el municipio de Guanaceví, Durango; y 3092 individuos de P. martinezii en la región de Tlatlauquitepec, Puebla, con plantas originadas de una mezcla de semillas colectadas de árboles al azar de poblaciones específicas.

scholarly journals Hot Workability of 300M Steel Investigated by In Situ and Ex Situ Compression Tests

Metals ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 880 ◽  
Author(s):  
Rongchuang Chen ◽  
Haifeng Xiao ◽  
Min Wang ◽  
Jianjun Li
Keyword(s):  
Flow Stress ◽  
Strain Rate ◽  
Hot Working ◽  
Ex Situ ◽  
Lower Strain Rate ◽  
Hot Workability ◽  
Compression Tests ◽  
300M Steel ◽  
Lower Strain

In this work, hot compression experiments of 300M steel were performed at 900–1150 °C and 0.01–10 s−1. The relation of flow stress and microstructure evolution was analyzed. The intriguing finding was that at a lower strain rate (0.01 s−1), the flow stress curves were single-peaked, while at a higher strain rate (10 s−1), no peak occurred. Metallographic observation results revealed the phenomenon was because dynamic recrystallization was more complete at a lower strain rate. In situ compression tests were carried out to compare with the results by ex situ compression tests. Hot working maps representing the influences of strains, strain rates, and temperatures were established. It was found that the power dissipation coefficient was not only related to the recrystallized grain size but was also related to the volume fraction of recrystallized grains. The optimal hot working parameters were suggested. This work provides comprehensive understanding of the hot workability of 300M steel in thermal compression.

Influence of in-situ and ex-situ Cu-Fe doping in K-OMS-2 catalysts on dye degradation via Fenton-like reaction with focus on catalytic properties and performances

2021 ◽  
Vol 23 ◽  
pp. 101030
Author(s):  
Kitirote Wantala ◽  
Totsaporn Suwannaruang ◽  
Janthip Palalerd ◽  
Prae Chirawatkul ◽  
Narong Chanlek ◽  
...  
Keyword(s):  
Catalytic Properties ◽  
Dye Degradation ◽  
Ex Situ ◽  
Fe Doping

scholarly journals Reproductive Anatomy of Chondrichthyans: Notes on Specimen Handling and Sperm Extraction. II. Sharks and Chimaeras

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2191
Author(s):  
Pablo García-Salinas ◽  
Victor Gallego ◽  
Juan F. Asturiano
Keyword(s):  
Artificial Insemination ◽  
Captive Breeding ◽  
Ex Situ ◽  
Specimen Handling ◽  
Viable Sperm ◽  
Abdominal Massage ◽  
Reproductive Anatomy ◽  
Conservation Projects ◽  
Breeding Techniques

The chondrichthyan fishes, which comprise sharks, rays, and chimaeras, are one of the most threatened groups of vertebrates on the planet. Given this situation, an additional strategy for the protection of these species could be the ex situ conservation projects developed in public aquaria and research centers. Nevertheless, to increase sustainability and to develop properly in situ reintroduction strategies, captive breeding techniques, such as sperm extraction and artificial insemination, should be developed. These techniques are commonly used in other threatened species and could be also used in chondrichthyans. However, the different reproductive morphologies found in this group can complicate both processes. Therefore, a comparison of the reproductive anatomy of eight distinct chondrichthyans, with an emphasis on those important differences when performing sperm extraction or artificial insemination, is carried out herein. Sharks and chimaeras belonging to the Scyliorhinidae, Carcharhinidae, Centrophoridae, Etmopteridae, Hexanchidae, and Chimaeridae families were obtained from commercial fisheries, public aquaria, and stranding events. In addition, the process of obtaining viable sperm samples through cannulation, abdominal massage, and oviducal gland extraction is described in detail for both living and dead animals.

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