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Microscope imaging technologies have turned out to yield an indispensable tool in modern biomedical research. Combined with fluorescence labeling techniques they not only provide new perspectives on tissues and cells as a whole, but also on processes at the cellular level, and will be one important experimental technique of systems biology. To handle this steadily increasing amount of image data, in this paper we propose a new and fully automatic approach for neurite segmentation and protein quantification. Our technique combines three phases of automatic neuron cell localization, neurite segmentation and protein analysis. In the second stage active contour models based on hierarchical gradient vector flow fields are employed, enabling precise neurite segmentation despite inhomogeneous texture. Neurite segmentation results as well as protein quantification profiles from a set of test images demonstrate the appropriateness of our approach for practical biomedical research.