This paper describes a novel device with high-throughput for evaluating an axonal transport and dynamics of acidic vesicles including autophagosomes in living neurons. A high-efficient and highthroughput device for axonal transport quantification is required to investigate the mechanisms of neurological disorders including amyotrophic lateral sclerosis (ALS). To this end, a novel device with superior usability is developed by integrating microgrooves on a cover glass using reactive ion etching (RIE).