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This paper reports on the development of an open-source image analysis software 'pipeline' dedicated to petrographic microscopy. Using conventional rock thin sections and images from a standard polarising microscope, the pipeline can classify minerals and subgrains into objects and obtain information about optic-axis orientation. Five metamorphic rocks were chosen to test and illustrate the method. Thin sections were imaged using reflected and cross- and plane-polarised transmitted light. Images were taken at different angles of the polariser and analyser (360° with 10° steps), both with and without the full-lambda plate. The resulting image stacks were analysed with a modular pipeline for optic-axis mapping (POAM). POAM consists of external and internal software packages that register, segment, classify, and interpret the visible light spectra using object-based image analysis (OBIAS). The mapped fields-of-view and grain orientation stereonets of interest are presented in the context of whole-slide images. Two innovations are reported. First, we used hierarchical tree region merging on blended multimodal images to classify individual grains of rock-forming minerals into objects. Second, we assembled a new optical mineralogy algorithm chain that identifies the mineral slow axis orientation. The c-axis orientation results were verified with scanning electron microscopy electron backscattered diffraction (SEM-EBSD) data. For quartz (uniaxial) in a granite mylonite the test yielded excellent correspondence of c-axis azimuth and good agreement for inclination. For orthorhombic orthopyroxene in a deformed garnet harzburgite, POAM produced acceptable results for slow axis azimuth. In addition, the method identified slight anisotropy in garnet that would not be appreciated by traditional microscopy. We propose that our method is ideally suited for two commonly performed tasks in mineralogy. First, for mineral grain classification of entire thin sections scans on blended images to provide automated modal abundance estimates and grain size distribution. Second, for prospective fields of view of interest, POAM can rapidly generate slow axis crystal orientation maps from multiangle image stacks on conventionally prepared thin sections for targeting detailed SEM-EBSD studies.
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BACKGROUND: Optical analysis of mineralized tissues with polarized microscopy is based on the mechanism of light interaction with biological tissues and spatial distribution of light. Understanding the light propagation mechanisms in mineralized tissues has huge clinical relevance in terms of esthetics and restoration. The present study aims to analyze the mineralogy characteristics of the cementoenamel junction (CEJ), which is a vital region involving merger of tissues with varied embryological origins. AIM: To analyze the mineralogy characteristics and CEJ patterns in deciduous teeth. OBJECTIVES: The variations of CEJ pattern in deciduous teeth and mineralogy characteristics such as retardation and birefringence are compared to the adjacent regions of underlying dentin corresponding to the permanent dentition. RESULTS: Mineralogy characteristics showed variation near the CEJ when compared to the adjacent regions of underlying dentin (statistically significant [P < 0.05]). When compared to permanent dentition, they showed a numerical difference, but the values were statistically insignificant. CEJ pattern analysis predominantly showed edge-to-edge interrelation, followed by root cementum overlapping the enamel and gap type. CONCLUSION: Analyzing CEJ in primary dentition is of paramount importance as it is a vulnerable zone in terms of caries progression and restorative margins. Increased edge-to-edge type of CEJ suggests a natural shield-like protection offered by enamel. Variations in mineralogy characteristics in the CEJ of deciduous dentition suggest the increased mineral content than in the adjacent regions of underling dentin. However, further investigations using advanced techniques for mineralogy analyses such as atomic force microscopy can help yield more intricacies of hard tissues of tooth.