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This paper presents a new system that reconstructs and visualizes 3D Purkinje cells (neurons) from two-photon microscopy images. The main components of the system are nonlinear diffusion filtering for denoising of each two-photon microscopy slice, increasing the image resolution of each Purkinje cell slice, global image enhancement of each slice as well as local pixel based image enhancement of each slice. Finally, 3D reconstruction and visualization of the Purkinje cell is accomplished using ImageJ. Computer simulations will illustrate the elucidated improvements over the original Purkinje cell images. Specifically, the presented system brought out hidden dendrite branches and allowed for a clearer picture of the entire Purkinje cell.