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Three-dimensional image analysis of high resolution confocal microscopy data of the Drosophila melanogaster brain

Chloé Isabelle Murtin 1, 2
2 Images et Modèles
CREATIS - Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé
Abstract : Although laser scanning microscopy is a powerful tool for obtaining thin optical sections, the possible depth of imaging is limited by the working distance of the microscope objective but also by the image degradation caused by the attenuation of both excitation laser beam and the light emitted from the fluorescence-labeled objects. Several workaround techniques have been employed to overcome this problem, such as recording the images from both sides of the sample, or by progressively cutting off the sample surface. The different views must then be combined in a unique volume. However, a straightforward concatenation is often not possible, because the small rotations that occur during the acquisition procedure, not only in translation along x, y and z axes but also in rotation around those axis, making the fusion uneasy. To address this problem we implemented a new algorithm called 2D-SIFT-in-3D-Space using SIFT (scale Invariant Feature Transform) to achieve a robust registration of big image stacks. Our method register the images fixing separately rotations and translations around the three axes using the extraction and matching of stable features in 2D cross-sections. In order to evaluate the registration quality, we created a simulator that generates artificial images that mimic laser scanning image stacks to make a mock pair of image stacks one of which is made from the same stack with the other but is rotated arbitrarily with known angles and filtered with a known noise. For a precise and natural-looking concatenation of the two images, we also developed a module progressively correcting the sample brightness and contrast depending on the sample surface. Those tools we successfully used to generate tridimensional high resolution images of the fly Drosophila melanogaster brain, in particular, its octopaminergic and dopaminergic neurons and their synapses. Those monoamine neurons appear to be determinant in the correct operating of the central nervous system and a precise and systematic analysis of their evolution and interaction is necessary to understand its mechanisms. If an evolution over time could not be highlighted through the pre-synaptic sites analysis, our study suggests however that the inactivation of one of these neuron types triggers drastic changes in the neural network.
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Chloé Isabelle Murtin. Three-dimensional image analysis of high resolution confocal microscopy data of the Drosophila melanogaster brain. Image Processing [eess.IV]. Université de Lyon, 2016. English. ⟨NNT : 2016LYSEI081⟩. ⟨tel-01715589⟩

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