Method For Morphometric Analysis Research Articles

Two methods for geometric morphometric analysis of trichodinids from killifishes.

In this study, we compared the efficacy of geometric morphometric techniques, including outlines and landmark-based approaches, to support the differentiation of Trichodina bellottii from three co-occurring killifish species. Both methods were able to differentiate trichodinids from different host species. However, discriminat analyses and MANOVA results based on landmarks had greater accuracy possibly because these analyses only provide information on certain points defined by the researcher, while the analyses based on outlines take into account points with less taxonomic information.

Setting the morphologic quality limits enabling accurate classification of charred archaeological grape seeds

This study investigates the morphological changes in grape pips resulting from various charring conditions. Employing high-resolution scanning combined with morphometric measurements for morphological analysis, we aimed to understand the effects of charring on grape pips. Our morphometric analysis demonstrated significant alterations in seed shape above 250 °C. The length–width ratio and the occurrence of cracks notably changed, providing a basis for assessing charring conditions. In addition, applying a machine learning classification method, we determined that accurate classification of grape varieties by the morphometric analysis method is feasible for seeds charred at up to 250 °C and 8 h. Integrating the morphometric changes and temperature ranges suitable for classification, we developed a sorting model for archaeological seeds. By projecting length–width ratios onto a curve calculated from controlled conditions, we estimated charring temperatures. Approximately 50% of archaeological seeds deviated from the model, indicating drastic charring conditions. This sorting model facilitates a stringent selection of seeds fit for classification, enhancing the accuracy of our machine learning-based methodology. In conclusion, combining machine learning with morphometric sorting enables the identification of charred grape seeds suitable for identification by the morphometric method. This comprehensive approach provides a valuable tool for future research for the identification of charred grape seeds found in archaeological contexts, enhancing our understanding of ancient viticulture practices and grape cultivation.

3D imaging and analysis to unveil the impact of microparticles on the pellet morphology of filamentous fungi.

Controlling the morphology of filamentous fungi is crucial to improve the performance of fungal bioprocesses. Microparticle-enhanced cultivation (MPEC) increases productivity, most likely by changing the fungal morphology. However, due to a lack of appropriate methods, the exact impact of the added microparticles on the structural development of fungal pellets is mostly unexplored. In this study synchrotron radiation-based microcomputed tomography and three-dimensional (3D) image analysis were applied to unveil the detailed 3D incorporation of glass microparticles in nondestructed pellets of Aspergillus niger from MPEC. The developed method enabled the 3D analysis based on 375 pellets from various MPEC experiments. The total and locally resolved volume fractions of glass microparticles and hyphae were quantified for the first time. At increasing microparticle concentrations in the culture medium, pellets with lower hyphal fraction were obtained. However, the total volume of incorporated glass microparticles within the pellets did not necessarily increase. Furthermore, larger microparticles were less effective than smaller ones in reducing pellet density. However, the total volume of incorporated glass was larger for large microparticles. In addition, analysis of MPEC pellets from different times of cultivation indicated that spore agglomeration is decisive for the development of MPEC pellets. The developed 3D morphometric analysis method and the presented results will promote the general understanding and further development of MPEC for industrial application.

Developing the Methods for Multidisciplinary Morphometric Analysis of Relief for Assessing the Tectonic Fragmentation of the Interior

Developing the Methods for Multidisciplinary Morphometric Analysis of Relief for Assessing the Tectonic Fragmentation of the Interior

Computer-Assisted Histopathological Calculation Analysis of the Sciatic Nerve of Diabetic Neuropathy Rat Model

Histopathology is the science that studies the signs of disease by studying the structural and functional changes that occur in cells using certain types of dyes such as hematoxylin and eosin (H&E). Traditionally histopathological testing is carried out using semi-quantitative methods. A more advanced method is done by taking photos digitally, and then digital photos are quantified with the help of software such as ImageJ using plug-in tools. Recent advances in digital pathology require the development of more efficient computerized image analysis such as the Gaussian adaptive threshold method. This research aims to compare the calculation results of computer-assisted digitalization of histopathology using the ImageJ plugin manual method with automatic calculations using Gaussian adaptive threshold to quantify the amount of sciatic nerve cell damage in the Diabetic peripheral neuropathy (DPN) rat model. In this study, two image analysis methods were used to test their ability to measure the amount of cell damage in the sciatic nerve of normal rats using a model of diabetic neuropathy. The first method uses the ImageJ plugin manual. The second method is the Gaussian adaptive threshold method. The ImageJ plugin manual method obtained a cell abnormality value of 213 cells. Meanwhile, with the Gaussian adaptive threshold method, a value of 204 cells was obtained. The calculation results of the two methods show an insignificant difference between the methods p >0.05. This study presents a computerized morphometric image analysis method with the potential for pathology digitalization applications.

Türkiye’den Salmo cinsine ait iki türün karşılaştırmalı otolit morfolojisi

In this study, the morphology of the sagittal otolith of Salmo coruhensis Turan, Kottelat & Engin, 2010 and Salmo fahrettini Turan, Kalayci, Bektaş, Kaya & Bayçelebi, 2020 from Çam Stream (Artvin) and Terme Stream (Samsun) was described by images of scanning electron microscopy. Its shape and contour were also analyzed with shape indices, elliptic Fourier coefficients and wavelet transforms. As the study material, a total of 30 S. coruhensis sample and 20 S. fahrettini sample were obtained. Interspecies differences in otolith shape and morphometry were evaluated by principal components analysis, canonical discrimination analysis, and permutational multivariate analysis of variance. The two salmonid species studied were distinguished by both morphometric and shape analysis methods. However, wavelet transform was found to be more effective than shape indices and elliptic Fourier coefficients in species discrimination, with an overall classification success rate of 80%. Our results showed that saccular otolith morphology could be an additional diagnostic character for trout species differentiation.

Estimation of the Ischemic Lesion in the Experimental Stroke Studies Using Magnetic Resonance Imaging (Review).

In translational animal study aimed at evaluation of the effectiveness of innovative methods for treating cerebral stroke, including regenerative cell technologies, of particular importance is evaluation of the dynamics of changes in the volume of the cerebral infarction in response to therapy. Among the methods for assessing the focus of infarction, MRI is the most effective and convenient tool for use in preclinical studies. This review provides a description of MR pulse sequences used to visualize cerebral ischemia at various stages of its development, and a detailed description of the MR semiotics of cerebral infarction. A comparison of various methods for morphometric analysis of the focus of a cerebral infarction, including systems based on artificial intelligence for a more objective measurement of the volume of the lesion, is also presented.

Enhancing structural plasticity of PC12 neurons during differentiation and neurite regeneration with a catalytically inactive mutant version of the zRICH protein

BackgroundStudies of the molecular mechanisms of nerve regeneration have led to the discovery of several proteins that are induced during successful nerve regeneration. RICH proteins were identified as proteins induced during the regeneration of the optic nerve of teleost fish. These proteins are 2’,3’-cyclic nucleotide, 3’-phosphodiesterases that can bind to cellular membranes through a carboxy-terminal membrane localization domain. They interact with the tubulin cytoskeleton and are able to enhance neuronal structural plasticity by promoting the formation of neurite branches.ResultsPC12 stable transfectant cells expressing a fusion protein combining a red fluorescent protein with a catalytically inactive mutant version of zebrafish RICH protein were generated. These cells were used as a model to analyze effects of the protein on neuritogenesis. Differentiation experiments showed a 2.9 fold increase in formation of secondary neurites and a 2.4 fold increase in branching points. A 2.2 fold increase in formation of secondary neurites was observed in neurite regeneration assays.ConclusionsThe use of a fluorescent fusion protein facilitated detection of expression levels. Two computer-assisted morphometric analysis methods indicated that the catalytically inactive RICH protein induced the formation of branching points and secondary neurites both during differentiation and neurite regeneration. A procedure based on analysis of random field images provided comparable results to classic neurite tracing methods.Graphical

Cardio-pulmonary nematodes of the red fox (Vulpes vulpes) of Sardinia, Italy

Cardio-pulmonary parasites, such as Angiostrongylus vasorum, Crenosoma vulpis, and Eucoleus aerophilus, pose a significant concern on account of pulmonary and cardiac problems they induce in dogs. While the red fox is known to be a key reservoir host for A. vasorum and may also play a role in transmitting C. vulpis and E. aerophilus, there has been no recent research on these parasites in foxes from Sardinia, with the most current studies dating back to 1986. A survey was conducted on red foxes in Sardinia, where a total of 51 foxes were collected, necropsied, and examined for adult worms in their hearts and lungs. The worms were identified using morphometric analysis and molecular methods. The results showed a 54.9% overall prevalence at dissection: 45.1% of the foxes were positive for E. aerophilus, 17.6% for C. vulpis, and 13.7% for A. vasorum. The molecular analyses validated the morphological characterization. In comparison to previous research, which found 13 out of 85 foxes to be positive for A. vasorum with a prevalence rate of 15.3% and 1 for E. aerophilus with a prevalence of 1.2%, this study showed an increased prevalence of E. aerophilus and C. vulpis, and a decrease in the prevalence of A. vasorum. These results indicate that the red foxes in Sardinia represent a reservoir host for cardio-pulmonary nematodes and it should be considered in the differential diagnosis of respiratory distress syndrome in dogs.

Shark mandible evolution reveals patterns of trophic and habitat-mediated diversification

Environmental controls of species diversity represent a central research focus in evolutionary biology. In the marine realm, sharks are widely distributed, occupying mainly higher trophic levels and varied dietary preferences, mirrored by several morphological traits and behaviours. Recent comparative phylogenetic studies revealed that sharks present a fairly uneven diversification across habitats, from reefs to deep-water. We show preliminary evidence that morphological diversification (disparity) in the feeding system (mandibles) follows these patterns, and we tested hypotheses linking these patterns to morphological specialisation. We conducted a 3D geometric morphometric analysis and phylogenetic comparative methods on 145 specimens representing 90 extant shark species using computed tomography models. We explored how rates of morphological evolution in the jaw correlate with habitat, size, diet, trophic level, and taxonomic order. Our findings show a relationship between disparity and environment, with higher rates of morphological evolution in reef and deep-water habitats. Deep-water species display highly divergent morphologies compared to other sharks. Strikingly, evolutionary rates of jaw disparity are associated with diversification in deep water, but not in reefs. The environmental heterogeneity of the offshore water column exposes the importance of this parameter as a driver of diversification at least in the early part of clade history.

Quantitative morphometric analysis in tibiofemoral joint osteoarthritis imaging: A literature review

ObjectiveTo highlight published quantitative morphometric analysis (QMA) methods for assessing tibiofemoral joint osteoarthritis in magnetic resonance imaging and computed tomography and underline the need for open and interoperable protocols for quantitative image analysis. DesignA literature search on PubMed/MEDLINE and Web of Science of keywords relating to QMA in magnetic resonance imaging and computed tomography in the context of tibiofemoral osteoarthritis in the past 23 years (2000–2022). The search was based on, but not limited to: “quantitative morphometric analysis” or “quantitative image analysis” in combination with “osteoarthritis”, “articular cartilage”, “subchondral bone”, “tibiofemoral joint”, “joint”, “CT”, and “MRI”. The search found 73 relevant publications that were manually screened and sorted for QMA methods. A further search to extract key functions of the underlying algorithms was performed. ResultMRI is generally used for QMA of articular cartilage and joint contact area, while CT is generally used for QMA of subchondral bone and joint space width. Studies have shown that QMA algorithms can be adapted to new tissues and modalities. However, many methods are not easily accessible, and there is fragmentation of computational tools and platforms in the research field. ConclusionQMA is an active research area, and many techniques from one modality can be readily extended to another. Adoption of open-source practices can allow algorithms developed for other imaging modalities to be shared, making it possible to bridge the knowledge gap for structures and pathological features for which QMA has not yet been investigated and to increase research output overall.

Морфометрическая характеристика ультраструктуры митохондрий легких крыс после введения животным хризотил асбеста

he method of morphometric analysis was used to study ultrastructural changes in the mitochondria of the lungs of rats after a single intratracheal injection of chrysotile-asbestos dust into animals at doses of 25 mg and 50 mg. According to morphometric parameters, more serious changes were detected in mitochondria under the influence of asbestos at a dose of 50 mg, which were characterized by a significant increase in the area, perimeter and average diameter of the outer and inner membranes. The value of the area of the outer membrane of mitochondria in intact animals was 0.38±0.02 µm2, the perimeter was 2.52±0.11 µm, the average diameter was 0.75±0.03 µm, for experimental rats (asbestos 50 mg) the data the indicators turned out to be significantly increased and amounted to 0.59±0.04 µm2 (the area of the outer membrane), the perimeter was 3.67±0.19 µm, and the average diameter was 1.06±0.05 µm. For the inner membrane, these indicators in the control were as follows: the area of the inner membrane was 0.33±0.02 µm2, the perimeter was 2.40±0.12 µm, the average diameter was 0.71±0.032 µm, and for asbestos at a dose of 50 mg: 0.56±0.05 µm2 (internal membrane area), perimeter 3.68±0.21 µm, mean diameter 1.06±0.06 µm. Under the action of asbestos in lung cells, a significant decrease in the length of mitochondrial cristae was revealed: 9.11 ± 0.41 μm (control, intact animals), asbestos at a dose of 25 mg: 4.07 ± 0.33 μm and asbestos at a dose of 50 mg: 2.34±0.20 µm. Swelling and destruction of the cristae is observed, and this can be traced by morphometric parameters of the cristae diameter, which accordingly increased under the influence of 50 mg of asbestos by 90.9% (p<0.001). The obtained values of the area of the inner and outer membranes, the diameter and length of mitochondrial cristae made it possible to assess the degree of ultrastructural disorders of mitochondria, which may indicate mitochondrial dysfunction under the action of asbestos.

Time-Lapse Imaging and Morphometric Analysis of Tracheal Development in Drosophila.

Detailed and quantitative analyses of the cellular events underlying the formation of specific organs or tissues is essential to understand the general mechanisms of morphogenesis and pattern formation. Observation of live tissues or whole-mount fixed specimens has emerged as the method of choice for identifying and quantifying specific cellular and tissular structures within the organism. In both cases, cell and subcellular structure identification and good quality image acquisition for these analyses are essential. Many markers for live imaging and fixed tissue are now available for detecting cell membranes, subcellular structures, and extracellular structures like the extracellular matrix (ECM). Combination of live imaging and analysis of fixed tissue is ideal to obtain a general and detailed picture of the events underlying embryonic development. By applying morphometric methods to both approaches, we can, in addition, obtain a quantitative evaluation of the specific parameters under investigation in morphogenetic and cell biological studies. In this chapter, we focus on the development of the tracheal system of Drosophila melanogaster, which provides an ideal paradigm to understand the formation of branched tubular organs. We describe the most used methods of imaging and morphometric analysis in tubulogenesis using mainly (but not exclusively) examples from embryonic development. We cover embryo preparation for fixed and live analysis of tubulogenesis, together with methods to visualize larval tracheal terminal cell branching and lumen formation. Finally, we describe morphometric analysis and quantification methods using fluorescent images of tracheal cells.

E15.5 Mouse Embryo Micro-CT Using a Bruker Skyscan 1172 Micro-CT.

X-ray computed microtomography (µCT) is a powerful tool to reveal the 3D structure of tissues and organs. Compared with the traditional sectioning, staining, and microscopy image acquisition, it allows a better understanding of the morphology and a precise morphometric analysis. Here, we describe a method for 3D visualization and morphometric analysis by µCT scanning of the embryonic heart of iodine-stained E15.5 mouse embryos.

Testing the Bordes method on handaxes: A geometric morphometric approach

Bordes’ typology has been in use for many years and is widely applied in studies of Early and Middle Palaeolithic stone tools, especially in vocabulary and typological classification in shaping artefacts (mainly flake tools and handaxes). However, over the years, this method has received different critiques, especially regarding the arbitrariness and subjectivism in the definition and classification of some artefacts. The application of geometric morphometric methods (2D or 3D) on the study of stone tools is starting to become widespread. These methodological approaches are highly suitable for measuring patterns in shape change between artefact groups, which would be impossible to establish with more “traditional” methods. This paper aims to analyse the accuracy and reliability of the main types of handaxes established by Bordes, by performing different methods of Geometric Morphometric Analysis. The evidence from this study suggests that a large percentage of the handaxe types noted by Bordes is reliable and correlates with statistically significant changes in shape and only a small percentage of forms have no geometric morphometric significance. Likewise, these findings support the suitability of Geometric Morphometric Analysis on lithic artefact assemblages focusing on the measurement and classification by shape changes.

Morphometric analysis for the sex determination of the skull of the Deltari Ilir dog (Canis lupus familiaris) of Kosovo.

This study aimed to explain the sex determination of the autochthonous dog Deltari Ilir with both morphometric and geometric analysis methods. For this purpose, 24 Deltari Ilir dog skulls (12 females and 12 males) were used in the study. The difference between males and females at 6 values was statistically significant. The most statistically significant difference was seen in the measurement of the greatest breadth of the occipital condyles (p < 0.000). This measurement was higher in male skulls. The next most significant difference was seen in the greatest inner height of the orbit measurement (p < 0.002). This measurement was also higher than for females. In general, the skull length measurements of male dogs were higher than that of females. Male dog skulls had greater skull length and skull height. The lateral view was used for geometric analysis and 14 landmarks were determined. As a result of principal component analysis, 22 PC values were obtained. PC1 accounted for 23.73% of the total variance. As a result of canonical variants analysis, it was observed that males and females were completely separated from each other. The caudal part of the males was wider than the females in geometric analysis. As a result of the study, sex-determining characteristics were revealed for the Deltari Ilir dog. It was seen that gender analysis could be done with both morphometric and geometric analysis methods. In addition, it was seen that morphometric results and geometric analysis results supported each other. Moreover, the results of the study will be useful in the function of comparative anatomy, in veterinary clinical practice, in zooarchaeology but why not also in the veterinary forensic investigation.

A computational framework for canonical holistic morphometric analysis of trabecular bone

Bone is a remarkable, living tissue that functionally adapts to external loading. Therefore, bone shape and internal structure carry information relevant to many disciplines, including medicine, forensic science, and anthropology. However, morphometric comparisons of homologous regions across different individuals or groups are still challenging. In this study, two methods were combined to quantify such differences: (1) Holistic morphometric analysis (HMA) was used to quantify morphometric values in each bone, (2) which could then be mapped to a volumetric mesh of a canonical bone created by a statistical free-form deformation model (SDM). Required parameters for this canonical holistic morphometric analysis (cHMA) method were identified and the robustness of the method was evaluated. The robustness studies showed that the SDM converged after one to two iterations, had only a marginal bias towards the chosen starting image, and could handle large shape differences seen in bones of different species. Case studies were performed on metacarpal bones and proximal femora of different primate species to confirm prior study results. The differences between species could be visualised and statistically analysed in both case studies. cHMA provides a framework for performing quantitative comparisons of different morphometric quantities across individuals or groups. These comparisons facilitate investigation of the relationship between spatial morphometric variations and function or pathology, or both.

Study of the tectonic structure and modern geodynamics of the nickel-copper-sulfide Kun-Manyo deposit at the stage of its field the development

Currently, the Kun-Manyo nickel-copper-sulfide deposit in the north of the Khabarovsk Krai is being prepared for development, with part of the reserves expected to be mined by underground mining. To justify the rational order of opening and excavation of sub-ore reserves it is necessary to have objective information on rock mass condition, which can be received as a result of complex geodynamic and geomechanical investigations.The established geodynamic position of the deposit, determined by its location at the junction of actively interacting large tectonic elements of the Euro-Asian tectonic plate – the tectonic stress of the North Asian craton and the Amur plate, as well as within the modern Olekmo-Stanovo seismic zone, has allowed the massif of the field area to be classified as tectonically stressed.An analysis of the data of the GPS-observation points on the territory of the Russian part of the Amur tectonic plate, the results of calculations of the vector field of velocities of modern movements of points, made within the framework of the ITRF – 2000 coordinate system, as well as the results of in-situ geomechanical studies of rock massifs of the Amur Plate’s rock-bump hazardous deposits, have made it possible to establish the current tectonic regime of the deposit area – a region of intense modern compression with a predicted intensity of more than 50 MPa. By methods of morphometric analysis and remote sensing, it has been found that the relative relief excesses were significant (700–1000 m), which may lead to an uncompensated horizontal component of geostatic stress. The most extended lineaments of the relief have predominantly southeasterly extension. The identified features of the tectonic structure and regional neotectonics have made it possible to determine the most probable direction and magnitude of the current main horizontal compression, which could be further used in solving various geomechanical problems in the exploitation of the field.

APPLICATION OF MORPHOMETRIC ANALYSIS FOR SMALL RIVER BASINS OF THE BAIKAL RIFT ZONE BASINS

The article discusses the use of morphometric analysis to study the features of formation and development of small river basins in the western branch of the Baikal rift zone basins (by example of the Ihe-Uhgun river basin). The author has prepared a hydrologically correct digital elevation model based on satellite data ALOS Digital Surface Model (DSM). A comprehensive assessment of the earth's surface was carried out, including for the purposes of geomorphological and hydrological analysis, as well as an automated calculation and mapping of standard morphometric indicators based on DEM data. The work is based on general physiographic research methods, the method of morphometric analysis of the relief using GIS, the method of geoinformation mapping. Statistical data of morphometric and hydrological indicators were collected using SAGA GIS, patterns of their distribution over the basin area were revealed, which, as a result, made it possible to draw conclusions about the factors and patterns of the river network development and determine the set of presented exogenous processes of relief formation in the Ihe-Uhgun river basin territory. The main factors in the small river basins development are: high base levels, complex tectonic structure of the territory, steep slopes and southern orientation of the slope exposure, etc. It was revealed that the geometry of the basin relief determines the direction and volume of surface runoff, as well as the intensity of exogenous geomorphological processes.

Building fuzzy areal geographical objects from point sets

AbstractRepresentations of fuzzy geographic objects and analyses of their spatial relationships have received considerable attention in the GIS and spatial database domains over the past 30 years. However, building fuzzy geographical objects from real data is still a challenge. Simple fuzzy areal object models are too restrictive for many applications, and general fuzzy areal models may not be restrictive enough; as a result, the extent of fuzzy regions that satisfy the relevant conditions may be too large to affect the location description and spatial analysis. A condition by which the number of cores is not greater than one is added for the general object model, and an operable method for constructing fuzzy objects from the point set is proposed. Two peak and pass sets are determined for the membership surface by the fuzzy morphometric analysis method. The first set is used to initially divide the footprint of the fuzzy surface into smaller subfootprints, and the second set is used to merge insignificant fuzzy objects with their nearest significant fuzzy objects; thus, unreasonable division is avoided. Cross‐validation is adopted to evaluate the generated fuzzy objects. An experiment is provided to verify the effectiveness of the proposed method.