Abstract
AbstractImage segmentation plays a crucial role in many medical imaging applications by automating or facilitating the delineation of anatomical structures. In the Drosophila brain research, the automatic segmentation of individual Drosophila brain neuropils from the large amount of experimental images is highly demanded because manual segmentation is a tedious and time consuming process. Mushroom bodies are the most important landmark in Drosophila brains. As a result, the automatic segmentation of mushroom bodies becomes a fundamental and significant step in establishing a standard landmark for the ensuing task of building a standard Drosophila brain model.In this thesis, we propose a system to accomplish the goal of automatic and accurate segmentation of mushroom bodies in given stacks of experimental images. The proposed system consists of two major steps—preprocessing and boundary extraction. On each image, a preprocessing procedure is performed, followed by the gradient vector flow snake (GVF snake) to define the final contours for segmenting. The preprocessing procedure includes the techniques of morphological smoothing, statistical thresholding, texture analysis and the fuzzy C-means algorithm. The goal of morphological smoothing and statistical thresholding methods is to remove the noise composed of the speckles near the mushroom bodies and the stained non-mushroom-body neuropils. The texture analysis and fuzzy c-means algorithm aim at sharpening the blurred boundaries of mushroom bodies especially around the calyx regions. We apply these techniques according to the contents of the processed images.The final contours of mushroom-body segmentation are extracted by the GVF snake algorithm. After the segmentation, most of the stained cells along with the noisy artifacts and neuropils other than mushroom bodies are cleaned away. The only human interaction required in our segmentation system is the selection of the real fore-four region among the segmented possible ones in the Calyxes region. Each slice containing images showing only the mushroom bodies can be used to construct a 3D model. From the experimental result, we have demonstrated that the proposed system can provide rapid segmentation and construction of individual 3D mushroom-body models. This system is proven instrumental in generating a more precise standard 3D Drosophila brain model, which is crucial in the Drosophila brain research.