scholarly journals Texture Feature Extraction From Microscope Images Enables Robust Estimation of ER Body Phenotype in Arabidopsis

2021 ◽  
Author(s):  
Arpan Kumar Basak ◽  
Mohamadreza Mirzaei ◽  
Kazimierz Strzałka ◽  
Kenji Yamada
Keyword(s):  
Robust Estimation ◽  
Cell Walls ◽  
Morphological Characteristics ◽  
Morphological Diversity ◽  
Objective Lens ◽  
Cell Organelle ◽  
Microscope Images ◽  
Cellular Components ◽  
Shape And Size ◽  
Cellular Organelles

Abstract Background: Cellular components are controlled by genetic and physiological factors that define their shape and size. However, quantitively capturing the morphological characteristics and movement of cellular organelles from micrograph images is challenging, because the analysis deals with complexities of images that frequently lead to inaccuracy in the estimation of the features. Here we show a unique quantitative method to overcome biases and inaccuracy of biological samples from confocal micrographs. Results: We generated 2D images of cell walls and spindle-shaped cellular organelles, namely ER bodies, with a maximum contrast projection of 3D confocal fluorescent microscope images. The projected images were further processed and segmented by adaptive thresholding of the fluorescent levels in the cell walls. Micrographs are composed of pixels, which have information on position and intensity. From the pixel information we calculated three types of features (spatial, intensity and Haralick) in ER bodies corresponding to segmented cells. The spatial features include basic information on shape, e.g., surface area and perimeter. The intensity features include information on mean, standard deviation and quantile of fluorescence intensities within an ER body. Haralick features describe the texture features, which can be calculated mathematically from the interrelationship between the pixel information. Together these parameters were subjected to multivariate analysis to estimate the morphological diversity. Additionally, we calculated the displacement of the ER bodies using the positional information in a time-lapse image. We captured similar morphological diversity and movement within ER body phenotypes on several microscopy experiments performed in different settings and scanned under different objectives. We then described differences in morphology and movement of ER bodies between A. thaliana wild type and mutants deficient in ER body-related genes. Conclusions: The findings unexpectedly revealed multiple genetic factors that are involved in the shape and size of ER bodies in A. thaliana. This is the first report showing morphological characteristics in addition to the movement of cellular components and quantitatively summarises plant phenotypic differences even in plants that show similar cellular components. The estimation of morphological diversity was independent of the cell staining method and the objective lens used in the microscopy. Hence, our study enables a robust estimation of plant phenotypes by recognizing small differences of complex cell organelle shapes and their movement, which is beneficial in a comprehensive analysis of the molecular mechanism for cell organelle formation that is independent of technical variations.

scholarly journals Texture feature extraction from microscope images enables a robust estimation of ER body phenotype in Arabidopsis

Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Arpan Kumar Basak ◽  
Mohamadreza Mirzaei ◽  
Kazimierz Strzałka ◽  
Kenji Yamada
Keyword(s):  
Robust Estimation ◽  
Cell Walls ◽  
Morphological Characteristics ◽  
Morphological Diversity ◽  
Objective Lens ◽  
Cell Organelle ◽  
Microscope Images ◽  
Cellular Components ◽  
Shape And Size ◽  
Cellular Organelles

Abstract Background Cellular components are controlled by genetic and physiological factors that define their shape and size. However, quantitively capturing the morphological characteristics and movement of cellular organelles from micrograph images is challenging, because the analysis deals with complexities of images that frequently lead to inaccuracy in the estimation of the features. Here we show a unique quantitative method to overcome biases and inaccuracy of biological samples from confocal micrographs. Results We generated 2D images of cell walls and spindle-shaped cellular organelles, namely ER bodies, with a maximum contrast projection of 3D confocal fluorescent microscope images. The projected images were further processed and segmented by adaptive thresholding of the fluorescent levels in the cell walls. Micrographs are composed of pixels, which have information on position and intensity. From the pixel information we calculated three types of features (spatial, intensity and Haralick) in ER bodies corresponding to segmented cells. The spatial features include basic information on shape, e.g., surface area and perimeter. The intensity features include information on mean, standard deviation and quantile of fluorescence intensities within an ER body. Haralick features describe the texture features, which can be calculated mathematically from the interrelationship between the pixel information. Together these parameters were subjected to multivariate analysis to estimate the morphological diversity. Additionally, we calculated the displacement of the ER bodies using the positional information in time-lapse images. We captured similar morphological diversity and movement within ER body phenotypes in several microscopy experiments performed in different settings and scanned under different objectives. We then described differences in morphology and movement of ER bodies between A. thaliana wild type and mutants deficient in ER body-related genes. Conclusions The findings unexpectedly revealed multiple genetic factors that are involved in the shape and size of ER bodies in A. thaliana. This is the first report showing morphological characteristics in addition to the movement of cellular components and it quantitatively summarises plant phenotypic differences even in plants that show similar cellular components. The estimation of morphological diversity was independent of the cell staining method and the objective lens used in the microscopy. Hence, our study enables a robust estimation of plant phenotypes by recognizing small differences in complex cell organelle shapes and their movement, which is beneficial in a comprehensive analysis of the molecular mechanism for cell organelle formation that is independent of technical variations.

Morphological peculiarities of seeds of some species of the genus Epipactis Zinn. (Orchidaceae Juss.) of Ukrainian flora

2019 ◽  
Vol 11 (1) ◽  
pp. 93-100
Author(s):  
T Ljubka ◽  
O Tsarenko ◽  
I Tymchenko
Keyword(s):  
Seed Coat ◽  
Cell Walls ◽  
Morphological Study ◽  
Population Level ◽  
Intercellular Spaces ◽  
Different Populations ◽  
Periclinal Walls ◽  
High Degree ◽  
Shape And Size ◽  
Generative Organs

The investigation of macro- and micromorphological peculiarities of seeds of four species of genus Epipactis (Orchidaceae) of Ukrainian flora were carried out. The genus Epipactis is difficult in the in in taxonomic terms and for its representatives are characterized by polymorphism of morphological features of vegetative and generative organs of plants and ability of species to hybridize. The aim of the research was to perform a comparative morphological study of seeds of E. helleborine, E. albensis, E. palustris, E. purpurata and to determine carpological features that could more accurately identify species at the stage of fruiting. A high degree of variation in the shape of the seeds in different populations within the species and overlap of most quantitative carpological characteristics of studied species are noted. There were no significant differences in micromorphological features of the structure of the testa at species or population level. The reticulate surface of the testa is characteristic of all species, the cells of testa are mostly elongated, penta-hexagonal, individual cells almost isodiametric-pentagonal. From the micropillary to the chalasal end, a noticeable change in the shape and size of the seed coat cells is not observed. There are no intercellular spaces, the anticlinal walls of adjacent cells are intergrown and the boundaries between them become invisible. The outer periclinal walls have a single, mainly longitudinal thin ribbed thickenings. Anticlinal cell walls are thick, dense, smooth. The longitudinal Anticlinal walls are almost straight, transverse - straight or sometimes curved in some cells. Epicuticular deposits on the periclinal walls are absent. It is concluded that the use of macro and micromorphological characteristics of seeds of these species for clearer diagnosis at the stage of fruiting is low informative.

scholarly journals Vertical clinging and leaping induced evolutionary rate shifts in postcranial evolution of tamarins and marmosets (Primates, Callitrichidae)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Léo Botton-Divet ◽  
John A. Nyakatura
Keyword(s):  
Elbow Joint ◽  
Evolutionary Rate ◽  
Large Diameter ◽  
Morphological Diversity ◽  
Locomotor Behavior ◽  
Shape Descriptors ◽  
High Affinity ◽  
Associated Species ◽  
Future Work ◽  
Shape And Size

Abstract Background Callitrichids comprise a diverse group of platyrrhine monkeys that are present across South and Central America. Their secondarily evolved small size and pointed claws allow them to cling to vertical trunks of a large diameter. Within callitrichids, lineages with a high affinity for vertical supports often engage in trunk-to-trunk leaping. This vertical clinging and leaping (VCL) differs from horizontal leaping (HL) in terms of the functional demands imposed on the musculoskeletal system, all the more so as HL often occurs on small compliant terminal branches. We used quantified shape descriptors (3D geometric morphometrics) and phylogenetically-informed analyses to investigate the evolution of the shape and size of the humerus and femur, and how this variation reflects locomotor behavior within Callitrichidae. Results The humerus of VCL-associated species has a narrower trochlea compared with HL species. It is hypothesized that this contributes to greater elbow mobility. The wider trochlea in HL species appears to correspondingly provide greater stability to the elbow joint. The femur in VCL species has a smaller head and laterally-oriented distal condyles, possibly to reduce stresses during clinging. Similarly, the expanded lesser trochanters visible in VCL species provide a greater lever for the leg retractors and are thus also interpreted as an adaptation to clinging. Evolutionary rate shifts to faster shape and size changes of humerus and femur occurred in the Leontocebus clade when a shift to slower rates occurred in the Saguinus clade. Conclusions Based on the study of evolutionary rate shifts, the transition to VCL behavior within callitrichids (specifically the Leontocebus clade) appears to have been an opportunity for radiation, rather than a specialization that imposed constraints on morphological diversity. The study of the evolution of callitrichids suffers from a lack of comparative analyses of limb mechanics during trunk-to-trunk leaping, and future work in this direction would be of great interest.

scholarly journals Landmark-based morphometry reveals phyllometric diversity along the shoot axis of the grapevine (Vitis vinifera L.)

2018 ◽  
Vol 14 (s1) ◽  
pp. 1-9
Author(s):  
Bodor Péter ◽  
Baranyai László ◽  
Szekszárdi Andrea ◽  
Bisztray György Dénes ◽  
Bálo Borbála
Keyword(s):  
Vitis Vinifera ◽  
Leaf Morphology ◽  
Morphological Characteristics ◽  
Morphological Diversity ◽  
Leaf Damage ◽  
Vitis Vinifera L ◽  
Graphic Software ◽  
High Diversity

Leaf morphology of the grapevine (Vitis vinifera L.) cv. ‘Kövidinka’ was evaluated based on 32 landmarks. The aim of this study was to reveal leaf morphological diversity along the shoot axis. For this purpose 10 shoots were collected with 26 to 35 leaves. Altogether 304 leaf samples were digitised and analysed with the GRA.LE.D 2.04. raster graphic software. Leaf damage was estimated based on the missing landmarks on the lamina. Our results showed that the leaves on the 11th and 13th nodes are the most intact, without missing landmarks. Lowest variability (cv = 0,126) of the investigated 54 morphological characteristics were observed among the leaves on the 11th nodes of the shoots, in accordance with the literature. Based on the results length of the veins, angles between the veins and further features such as size of the serrations show high diversity along the shoot axis. These results underline the need of careful sampling during the ampelometric investigations.

New data on gastropod genus Hirsuticyclus (Caenogastropoda, Cyclophoridae) from mid-Cretaceous Kachin amber

2021 ◽  
pp. SP521-2021-127
Author(s):  
Tingting Yu
Keyword(s):  
New Species ◽  
Type Species ◽  
Morphological Characteristics ◽  
Morphological Diversity ◽  
First Record ◽  
Land Snail ◽  
Generic Diagnosis ◽  
Burmese Amber ◽  
New Material ◽  
A New Species

AbstractThe genus Hirsuticyclus Neubauer, Xing & Jochum, 2019 was the first record of an exceptionally preserved land snail with dense periostracal hairs from mid-Cretaceous Kachin (Burmese) amber. Here we document four newly-discovered shells from Kachin amber, one belonging to the type species Hirsuticyclus electrum Neubauer, Xing & Jochum, 2019 and the remaining three shells belonging to a new species, Hirsuticyclus canaliculatus sp. nov. Well-preserved morphological characteristics of these two species could be clearly demonstrated under light microscopy combined with modern micro-CT scans with computer 3D reconstructions. Our new material of the type species amends the generic diagnosis based on a better-preserved shell including the peristome and operculum. The new species shows distinctive shell characteristics such as numerous spiral keels and a flaring, folded peristome interrupted by two canals. These excellently preserved fossils contribute to our understanding of the morphological diversity and evolution of these ancient members of cyclophoroids.

scholarly journals Morphological diversity of the stone crayfish − traditional and geometric morphometric approach

2019 ◽  
pp. 1 ◽  
Author(s):  
Leona Lovrenčić ◽  
Vjera Pavić ◽  
Stefan Majnarić ◽  
Lucija Abramović ◽  
Mišel Jelić ◽  
...  
Keyword(s):  
Morphological Variability ◽  
Morphological Characteristics ◽  
Morphological Diversity ◽  
Dorsal Side ◽  
Small Scale ◽  
Geometric Morphometric ◽  
Discriminant Analyses ◽  
Stone Crayfish ◽  
Multivariate Discriminant ◽  
First Time

Austropotamobius torrentium is one of four native European crayfish species inhabiting Croatian freshwaters. Existence of eight divergent monophyletic mtDNA phylogroups was described within A. torrentium; six of them are distributed in Croatia, with the highest genetic diversity established in its northern-central Dinaric region. Recent small-scale study of the stone crayfish morphological variability indicated significant differences among different phylogroups. In the present study larger sample size, covering populations from five phylogroups, was analysed with the aim of determining whether there are morphological characteristics that reliably separate stone crayfish from different phylogroups. Aiming this, 245 stone crayfish were analysed through traditional (TM) and, for the first time, geometric morphometric (GM) analyses. Multivariate discriminant analyses included 24 TM characteristics per crayfish, while GM comprised analyses of 22 landmarks on the dorsal side of cephalon. Both methods revealed congruent results, and significant differences among phylogroups in analysed features were obtained, with the cephalon shape contributing the most to crayfish discrimination. Research confirmed that both approaches, combined with statistical methods, are useful in distinguishing and separating crayfish phylogroups. Findings of present study are compatible with the previous molecular findings; stone crayfish present several distinct evolutionary lineages whose species status are currently undefined and require urgent clarification.

scholarly journals Morphological Characteristics of Dimples of Ductile Fracture of VT23M Titanium Alloy and Identification of Dimples on Fractograms of Different Scale

Materials ◽  
2019 ◽  
Vol 12 (13) ◽  
pp. 2051 ◽  
Author(s):  
Ihor Konovalenko ◽  
Pavlo Maruschak ◽  
Janette Brezinová ◽  
Jozef Brezina
Keyword(s):  
Titanium Alloy ◽  
Ductile Fracture ◽  
Digital Images ◽  
Morphological Characteristics ◽  
Automated Detection ◽  
Fracture Mechanisms ◽  
Test Results ◽  
High Quality ◽  
Quality Requirements ◽  
Shape And Size

The authors developed a method for the automated detection and calculation of quantitative parameters of dimples of ductile fracture on the digital images of fracture surfaces obtained at different scales. The processing algorithm of fractographic images was proposed, which allowed high quality recognition of the shape and size of dimples to be achieved, taking into account the morphological features of their digital images. The developed method for identifying dimples of various physical and morphological characteristics was tested on the VT23M alloy. The test results showed that the method meets the quality requirements for the automated diagnostics of fracture mechanisms of titanium alloys.

scholarly journals A Probabilistic Statistical Method for the Determination of Void Morphology with CFD-DEM Approach

Energies ◽  
2020 ◽  
Vol 13 (16) ◽  
pp. 4041
Author(s):  
Yuanxiang Lu ◽  
Sihan Liu ◽  
Xinru Zhang ◽  
Zeyi Jiang ◽  
Dianyu E
Keyword(s):  
Probabilistic Method ◽  
Gas Injection ◽  
Morphological Characteristics ◽  
Packed Bed ◽  
Two Dimensional ◽  
Two Phase ◽  
Binary Images ◽  
Void Shape ◽  
Shape And Size

Voids that are formed by gas injection in a packed bed play an important role in metallurgical and chemical furnaces. Herein, two-phase gas–solid flow in a two-dimensional packed bed during blast injection was simulated numerically. The results indicate that the void stability was dynamic, and the void shape and size fluctuated within a certain range. To determine the void morphology quantitatively, a probabilistic method was proposed. By statistically analyzing the white probability of each pixel in binary images at multiple times, the void boundaries that correspond to different probability ranges were obtained. The boundary that was most appropriate with the simulation result was selected and defined as the well-matched void boundary. Based on this method, the morphologies of voids that formed at different gas velocities were simulated and compared. The method can help us to express the morphological characteristics of the dynamically stable voids in a numerical simulation.

scholarly journals Monitoring Fungicide Sensitivity Levels and Mycelial Compatibility Groupings of Sclerotium rolfsii Isolates from Florida Peanut Fields

2017 ◽  
Vol 44 (2) ◽  
pp. 83-92 ◽  
Author(s):  
K. Khatri ◽  
S. Kunwar ◽  
R. L. Barocco ◽  
N. S. Dufault
Keyword(s):  
Management Practices ◽  
Phenotypic Diversity ◽  
Sclerotium Rolfsii ◽  
Morphological Characteristics ◽  
Morphological Diversity ◽  
Fungicide Sensitivity ◽  
Dose Effects ◽  
Mycelial Compatibility ◽  
Monitoring Survey ◽  
High Level

ABSTRACT Sclerotium rolfsii, the causal agent of peanut stem rot, is a diverse pathogen that has exhibited decreases in sensitivity to fungicides in areas where they are frequently applied. To better understand this pathogen's diversity and its response to various fungicides in Florida, a monitoring survey was done to examine isolates from several peanut producing areas using morphological characteristics, mycelial compatibility groupings and fungicide sensitivity profiles. A high level of morphological diversity was observed among a small number (N = 15) of isolates which was affirmed by both Shannon-Weiner (E = 0.812) and Simpson's (D = 0.280) indices. However, despite this high level of diversity, fungicide sensitivity of these isolates to flutolanil (EC50 = 0.031 ppm) and tebuconazole (EC50 = 0.008 ppm) appears to remain relatively unchanged when compared to a previous baseline study. Utilizing a small number of isolates, this monitoring survey indicated the EC50 values for the products azoxystrobin (EC50 = 0.050 ppm), prothioconazole (EC50 = 0.213 ppm), penthiopyrad (EC50 = 0.016 ppm) and solatenol (EC50 = 0.005 ppm). A trend for hormesis was also noted in this survey (e.g. flutolanil), but further research is necessary to better understand sub-lethal fungicide dose effects on increasing mycelial growth. It is apparent from these results that despite the high levels of phenotypic diversity in S. rolfsii populations, current fungicide management practices should remain effective for disease control.

Electron microscopic observations of infection threads in driselase treated nodules of Astragalus sinicus

1986 ◽  
Vol 32 (12) ◽  
pp. 947-952 ◽  
Author(s):  
Shiro Higashi ◽  
Kazuya Kushiyama ◽  
Mikiko Abe
Keyword(s):  
Cell Wall ◽  
Cell Walls ◽  
Plant Cell Wall ◽  
Root Nodules ◽  
Morphological Characteristics ◽  
Enzyme Treatment ◽  
Vascular Bundles ◽  
Electron Microscopic ◽  
Astragalus Sinicus ◽  
Infection Threads

The morphological characteristics of infection threads in the root nodules of Astragalus sinicus were examined by scanning and transmission electron microscopy. The infection threads, epidermal cell walls, and vascular bundles of the nodule were not altered when a nodule was treated with driselase (a plant cell wall degrading enzyme), although the cell walls of meristematic and bacteroid-including zones were completely decomposed by the enzyme treatment. Some infection threads were funnel shaped at the site of attachment of the infection thread to the host cell wall.

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