Mitochondria is an important organelle for maintaining cells such as neurons’ physiological processes. Mitochondrial transport is known to be strongly related to neurodegenerative disease of the central nervous system such as Alzheimer’s disease and Parkinson’s disease. Thus, many researchers are interested in mitochondrial transport. Unfortunately, there is no automated tool to analyze the movement and thus correlate them with cellular characteristics. In this paper, we develop a mask-rendering tool and two-dimensional visualization tool based on a slice for analysis of mitochondrial transports using the Visualization Toolkit (VTK).