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This work proposes an analytical method to identify plant species based on microscopy images of the midrib cross-section of leaves. Unlike previous shape-based approaches based on the individual shape of external contours and cells, an architectural analysis is proposed, where the midrib is semi-automatically segmented and partitioned into histologically relevant structures composed of layers of cells and vascular structures. Using a sequence of morphological operations, a set of geometrical measures from the cells in each layer is extracted to produce a vector of features for species categorization. The method applied to a database containing 10 species of plants from the Brazilian flora achieved a success rate of 91.7%, outperforming other classical shape-based approaches published in the literature. Key words: automatic species identification, image analysis, morphological features. Les auteurs de ce travail proposent une methode analytique permettant d'identifier une espece vegetale a partir d'images en microscopie de coupes transversales de la nervure mediane des feuilles. Contrairement aux approches precedentes basees sur la forme qui reposent sur la forme individuelle des contours externes et sur les cellules, une analyse architecturale est proposee, dans laquelle la nervure mediane est segmentee de maniere semi-automatique et divisee en structures histologiquement pertinentes composees de couches cellulaires et de structures vasculaires. En utilisant une sequence d'operations morphologiques, une serie de mesures geometriques des cellules de chaque couche est extraite afin de produire un ensemble de caracteristiques pour categoriser les especes. La methode appliquee a une base de donnees contenant 10 especes de plantes issues de la flore du Bresil a obtenu un taux de succes de 91.7%, surpassant les autres approches classiques basees sur la forme publiees dans la litterature. [Traduit par la Redaction] Mots-cles : identification automatisee d'une espece, analyse d'image, caracteristiques morphologiques., Introduction The categorization of plants into species is an important taxonomical task; it provides meaningful information about particular characteristics of a species, which can be used in the context of [...]

Caries is a chronic disease that causes the alteration of the structure of dental tissues by acid dissolution (in enamel, dentine and cementum) and proteolytic degradation (dentine and cementum) and generates an important cost of care. There is a need to visualise and characterise the acid dissolution process on enamel due to its hierarchical structure leading to complex structural modifications. The process starts at the enamel surface and progresses into depth, which necessitates the study of the internal enamel structure. Artificial demineralisation is usually employed to simulate the process experimentally. In the present study, the demineralisation of human enamel was studied using surface analysis carried out with atomic force microscopy as well as 3D internal analysis using synchrotron X-ray tomography during acid exposure with repeated scans to generate a time-lapse visualisation sequence. Two-dimensional analysis from projections and virtual slices and 3D analysis of the enamel mass provided details of tissue changes at the level of the rods and inter-rod substance. In addition to the visualisation of structural modifications, the rate of dissolution was determined, which demonstrated the feasibility and usefulness of these techniques. The temporal analysis of enamel demineralisation is not limited to dissolution and can be applied to other experimental conditions for the analysis of treated enamel or remineralisation. [ABSTRACT FROM AUTHOR]

Hard dental tissues possess a complex hierarchical structure that is particularly evident in enamel, the most mineralised substance in the human body. Its complex and interlinked organisation at the Ångstrom (crystal lattice), nano-, micro-, and macro-scales is the result of evolutionary optimisation for mechanical and functional performance: hardness and stiffness, fracture toughness, thermal, and chemical resistance. Understanding the physical–chemical–structural relationships at each scale requires the application of appropriately sensitive and resolving probes. Synchrotron X-ray techniques offer the possibility to progress significantly beyond the capabilities of conventional laboratory instruments, i.e., X-ray diffractometers, and electron and atomic force microscopes. The last few decades have witnessed the accumulation of results obtained from X-ray scattering (diffraction), spectroscopy (including polarisation analysis), and imaging (including ptychography and tomography). The current article presents a multi-disciplinary review of nearly 40 years of discoveries and advancements, primarily pertaining to the study of enamel and its demineralisation (caries), but also linked to the investigations of other mineralised tissues such as dentine, bone, etc. The modelling approaches informed by these observations are also overviewed. The strategic aim of the present review was to identify and evaluate prospective avenues for analysing dental tissues and developing treatments and prophylaxis for improved dental health. [ABSTRACT FROM AUTHOR]

Background: Primordial odontogenic tumour is a benign mixed neoplasm of recent description, which has histological similarities with other odontogenic tumours such as the ameloblastic fibroma. In this article, we investigate the architecture of the sub‐epithelial layer of mesenchymal cells expressing the marker CD34 in primordial odontogenic tumour. Objective: Analyse the spatial patterns of CD34 expression in primordial odontogenic tumour and compare them with those in ameloblastic fibroma and the normal tooth germ by means of objective imaging approaches, to better characterise these lesions. Methods: Two cases of primordial odontogenic tumour, four cases of ameloblastic fibroma and two cases of tooth germ in cap and bell stages were used for morphological, structural and immunohistochemical analyses. Results: CD34 expression was found in vascular endothelium of primordial odontogenic tumour, ameloblastic fibroma and tooth germ. In addition, a characteristic sub‐epithelial expression was observed only in primordial odontogenic tumour, corresponding to 84%–86% of the sample boundaries. Moreover, the zone expressing CD34 corresponded with a higher cellularity, which was absent in ameloblastic fibroma and tooth germ. Conclusion: Image analysis of the primordial odontogenic tumour architecture revealed characteristics absent in other odontogenic tumours and tooth germs. This study provides additional information to support the idea that this neoplasm is a distinct entity from early stage AF or developing odontoma. [ABSTRACT FROM AUTHOR]

Abstract Background This paper describes a quantitative analysis of the cyst lining architecture in radicular cysts (of inflammatory aetiology) and odontogenic keratocysts (thought to be developmental or neoplastic) including its 2 counterparts: solitary and associated with the Basal Cell Naevus Syndrome (BCNS). Methods Epithelial linings from 150 images (from 9 radicular cysts, 13 solitary keratocysts and 8 BCNS keratocysts) were segmented into theoretical cells using a semi-automated partition based on the intensity of the haematoxylin stain which defined exclusive areas relative to each detected nucleus. Various morphometrical parameters were extracted from these "cells" and epithelial layer membership was computed using a systematic clustering routine. Results Statistically significant differences were observed across the 3 cyst types both at the morphological and architectural levels of the lining. Case-wise discrimination between radicular cysts and keratocyst was highly accurate (with an error of just 3.3%). However, the odontogenic keratocyst subtypes could not be reliably separated into the original classes, achieving discrimination rates slightly above random allocations (60%). Conclusion The methodology presented is able to provide new measures of epithelial architecture and may help to characterise and compare tissue spatial organisation as well as provide useful procedures for automating certain aspects of histopathological diagnosis.

Acid-induced enamel demineralisation affects many individuals either by exposure to acidic diets, acidic gas pollution (dental erosion) or to dental plaque acids (dental caries). This study aimed to develop in situ X-ray and light imaging methods to determine progression of enamel demineralisation and the dynamic relationship between acid pH and mineral density. Hourly digital microradiograph time-lapse sequences showed the depth of enamel demineralisation in 500 µm thick sections progressed with time from the surface towards the dentine following a power-law function, which was 21% faster than the lateral demineralisation progression after exposure for 85 h to lactic acid (10%, pH 2.2). The minimum greyscale remaining (mineral content) within the induced enamel lesion followed an exponential decay, while the accumulated total greyscale loss with time was linear, which showed a constant anisotropic mineral release within the enamel architecture. This 85 h demineralisation method studied by polarised light microscopy time-lapse sequences showed that once the demineralisation front reached the enamel Hunter-Schreger bands, there was preferential demineralisation along those bands. Mineral density loss was linear with increasing pH acidity between pH 5.2 and pH 4.0 (with 0.4 pH increments) when incubated over a 3-week period exposed to 0.5% lactic acid. At pH 4.0, there was complete mineral loss in the centre of the demineralised area after the 3-week period and the linear function intercepted the x-axis at ~ pH 5.5, near the critical pH for hydroxyapatite (HAp). These observations showed how intrinsic enamel structure and pH affected the progression of demineralisation. Hydroxyapatite crystallites (HAp) in human enamel dissolve when exposed to an acidic environment but little is known about how the intrinsic structures in enamel and pH influence the demineralisation kinetics. We have developed a time-lapse in situ microradiography method to quantify microscopic anisotropic mineral loss dynamics in response to an acid-only caries model. Correlation with polarised light microscopy time-lapse sequences showed that larger structures in enamel also influence demineralisation progression as demineralisation occurred preferentially along the Hunter-Schreger bands (decussating prismatic enamel). The pH-controlled enamel mineral release in a linear manner quantifying the relationship between HAp orientation and acid solubility. These findings should direct the development of improved anti-demineralisation/ remineralisation treatments to retain/ restore the natural intrinsic enamel structure. Image, graphical abstract [ABSTRACT FROM AUTHOR]

Introduction: Applying load to an ultrasonic scaler tip can affect its vibrations. Cooling water flowing over such tips will also act as a load - though this is rarely considered in in vitro research investigations. The aim of this study was to determine the effect of water flow rate on ultrasonic scaler vibration. Study design: The vibration displacement amplitude of three designs of scaler insert, including a Slimline tip, TFI-10 and TFI-3 (Dentsply, USA), were assessed unloaded and under 0.50 N and 1.00 N load and with water flow rates of 20 ml/min and 40 ml/min. Vibration analysis was performed using a scanning laser vibrometer. Results: Increasing water flow rate from 20 ml/min to 40 ml/min caused a significant decrease (p < 0.0001) in all tip vibrations. Increasing water from 20 ml/min to 40 ml/min with the unloaded Slimline tip is equivalent to applying a 1.00 N load, and for the TFI-10 tip is equivalent to applying a 0.50 N load in vitro. Conclusions: Water flow rate has a significant influence on scaler tip vibration characteristics and is particularly important for lighter, thinner tips such as the Slimline design. Future in vitro research must consider the loading effect that water flow over ultrasonic scaler tips will have on their performance. [ABSTRACT FROM AUTHOR]

Objective: To examine the influence of compressive and deflective force on the filaments of 7 commercially available powered toothbrushes. Method and Materials: The deformation (collapse under force) of the filaments on individual brush heads was measured at a rate of 4 mm/mm using an Instron load testing machine under applied loads of 0.5 to 3.0 N. The load was directed perpendicular to the long axis of the filaments. The peak deflection force (deflecting of the filaments from their normal position) was measured with the head of the powered brush oriented horizontally to the applied load. Measurements were taken while the brush head was stationary and during oscillation. Data for peak deflective force were analyzed using a general linear model with post hoc Tukey tests. Results: All powered toothbrushes showed filament deformation when increasing loads were applied. Deformation of the filaments was greatest at 0.5 N and 1.0 N for the Teledyne and was recorded at 1.70 mm and 3.67 mm, respectively. At 2.0 N, greater deformation (5.50 mm) occurred with the Blend-a-Dent, and at 3.0 N, the Sonicare powered toothbrush exhibited a deformation of 3.95 mm. Over the whole range of applied forces, the Braun D15 showed the lowest deformation effects. The different deformations of the filaments recorded between the heads of all powered toothbrushes tested were significant (general linear model, P < .001). Also a decrease in peak deflective force was observed between stationary and oscillating toothbrush heads. Conclusions: The compressive and peak deflective forces vary between different brushes, and the ability to resist deformation depends on the arrangement of the filaments on the head of the powered brush. [ABSTRACT FROM AUTHOR]

We present an unsupervised segmentation framework featuring multiscale superpixels and k-means clustering to identify image data belonging to three distinct regions of interest: epithelium, stroma and background in H&E stained sections of oropharyngeal cancer micro-arrays. The method could be used as an exploratory tool for image contents and for semi-automated image annotation by providing a first automated approximation that expert operators can later refine and approve. [ABSTRACT FROM AUTHOR]

Motivation Microscopy images of stained cells and tissues play a central role in most biomedical experiments and routine histopathology. Storing colour histological images digitally opens the possibility to process numerically colour distribution and intensity to extract quantitative data. Among those numerical procedures are colour deconvolution, which enable decomposing an RGB image into channels representing the optical absorbance and transmittance of the dyes when their RGB representation is known. Consequently, a range of new applications become possible for morphological and histochemical segmentation, automated marker localization and image enhancement. Availability and implementation Colour deconvolution is presented here in two open-source forms: a MATLAB program/function and an ImageJ plugin written in Java. Both versions run in Windows, Macintosh and UNIX-based systems under the respective platforms. Source code and further documentation are available at: https://blog.bham.ac.uk/intellimic/g-landini-software/colour-deconvolution-2/. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Dental caries is one of the most common chronic diseases that affect human teeth. It often initiates in enamel, undermining its mechanical function and structural integrity. Little is known about the enamel demineralisation process caused by dental caries in terms of the microstructural changes and crystallography of the inorganic mineral phase. To improve the understanding of the carious lesion formation process and to help identify efficient treatments, the evolution of the microstructure at the nano-scale in an artificially induced enamel erosion region was probed using advanced synchrotron small-angle and wide-angle X-ray scattering (SAXS and WAXS). This is the first in vitro and time-resolved investigation of enamel demineralisation using synchrotron X-ray techniques which allows in situ quantification of the microstructure evolution over time in a simulated carious lesion. The analysis revealed that alongside the reduction of mineral volume, a heterogeneous evolution of hydroxyapatite (HAp) crystallites (in terms of size, preferred orientation and degree of alignment) could be observed. It was also found that the rate and direction of dissolution depends on the crystallographic orientation. Based on these findings, a novel conceptual view of the process is put forward that describes the key structural parameters in establishing high fidelity ultrastructure-based numerical models for the simulation of the enamel demineralisation process. Statement of significance Hydroxyapatite (HAp) crystallites in the enamel dissolve during dental caries although little is known about the structural-chemical relationships that control the dynamic demineralisation process. For the first time this work investigated the in situ evolution of nano-scale morphology and the spatial distribution of ultrastructural HAp crystallites of human enamel during demineralisation in simulated caries. Advanced synchrotron SAXS and WAXS techniques showed that the heterogeneous evolution of crystallites (size, preferred orientation and degree of alignment) could be attributed to crystallographic-orientation-dependent anisotropic dissolution. Hence we propose a novel conceptual schematic diagram to describe the demineralisation process. These findings have important implications for understanding the detailed mechanisms of enamel demineralisation and provide insight into potential enamel remineralisation that could restore structural integrity and function. [ABSTRACT FROM AUTHOR]

Algorithmic segmentation of histologically relevant regions of tissues in digitized histopathological images is a critical step towards computer-assisted diagnosis and analysis. For example, automatic identification of epithelial and stromal tissues in images is important for spatial localisation and guidance in the analysis and characterisation of tumour micro-environment. Current segmentation approaches are based on supervised methods, which require extensive training data from high quality, manually annotated images. This is often difficult and costly to obtain. This paper presents an alternative data-independent framework based on unsupervised segmentation of oropharyngeal cancer tissue micro-arrays (TMAs). An automated segmentation algorithm based on mathematical morphology is first applied to light microscopy images stained with haematoxylin and eosin. This partitions the image into multiple binary ‘virtual-cells’, each enclosing a potential ‘nucleus’ (dark basins in the haematoxylin absorbance image). Colour and morphology measurements obtained from these virtual-cells as well as their enclosed nuclei are input into an advanced unsupervised learning model for the identification of epithelium and stromal tissues. Here we exploit two Consensus Clustering (CC) algorithms for the unsupervised recognition of tissue compartments, that consider the consensual opinion of a group of individual clustering algorithms. Unlike most unsupervised segmentation analyses, which depend on a single clustering method, the CC learning models allow for more robust and stable detection of tissue regions. The proposed framework performance has been evaluated on fifty-five hand-annotated tissue images of oropharyngeal tissues. Qualitative and quantitative results of the proposed segmentation algorithm compare favourably with eight popular tissue segmentation strategies. Furthermore, the unsupervised results obtained here outperform those obtained with individual clustering algorithms. [ABSTRACT FROM AUTHOR]

Haemic neoplasia (HN) in bivalves has been reported in association with mass mortality events in various species of molluscs. The aim of this work was to quantify the nuclear morphometry and DNA content of neoplastic cells of mussels Mytilus galloprovincialis affected by HN using nuclear densitometry in Feulgen-stained preparations. The results were also compared with a population of normal mussel haemocytes. We captured 256 images of 3 different neoplasia stages and 120 images of normal haemocytes; thus, a total of 120,166 nuclei were analysed. We extracted 21 morphological parameters from normal and neoplastic nuclei. Eighteen of these parameters were different (P<0.05). Among those (expressed in pixel units—inter-pixel distance of 0.45 micrometres—as: normal vs. neoplastic) nuclear area (117.1±94.1 vs. 423.1±226.9), perimeter (44.9±14.0 vs. 79.0±21.3) and (IOD) integrated optical density (13.47±34.5 vs. 177.1±150.8) were relevant features to discriminate between normal and neoplastic cells. Those differences allowed identifying two distinctive populations of neoplastic nuclei, occasionally in the same individuals at a given phase of the disease. Moreover, neoplastic haemocytes in less extended lesions showed a ploidy value of 6.2 n along with the presence of a second population of circulating cells with a DNA content of 10.7n. In samples with moderate disease only one peak at 7n was observed. Finally, in more severe conditions, a further ploidy peak of 7.8n was recorded, accompanied by a shallow but broad peak of 31n. This latter extreme value is thought to be due to the presence of giant multinucleated cells where individual nuclei overlap in space and cannot be discerned individually. Computer-based imaging allowed the direct visualization of the cell populations and simultaneous collection of ploidy data as well as morphological features of nuclei. [ABSTRACT FROM AUTHOR]