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Recently developed were the Brainbow and Flybow techniques that can image and visualize a large number of neurons simultaneously; however, scientists still lack adequate tools to process this kind of colored multi-neuron image volumes. Due to dozens of colorized neuron fibers spreading densely in a very intricate structure, it is difficult to trace them by existing algorithms designed for single-neuron images. We proposed a framework to formulate and solve this issue, and the experimental results show that our method can successfully extract independent neurons from Flybow images. Consequently, the proposed procedure contributes to neuroscience by increasing the efficiency of collecting neuron information from Flybow images.