Apart from a year in Tokyo from 1953 to 1954, Shinya has spent the rest of his scientific career in the United States. After he returned from Tokyo, he took a position at the University of Rochester in New York State. While at Rochester, Inoué designed a new Shinya-scope, which was built in the instrument shop at the Institute of Optics. The technicians built it to last with high quality components, so this new microscope lasted well over four decades in active use.
After he moved to Dartmouth College, Shinya worked out a new way of using ultraviolet (UV) light in microscopy, and developed a method to analyse the changes in birefringence in the sperm heads of cave crickets. This research demonstrated how DNA was packed into the sperm heads, and he interpreted this in terms of the structure of DNA, complementing molecular biological inquiries into that vital molecule.
In 1966, Shinya left Dartmouth for the University of Pennsylvania. In the summer of 1967, he became a Special Lecturer in the Physiology course at the MBL. After a lecture in the morning, he would work with students in the lab, sometimes until late at night. Shinya relished the intensive and communal nature of the research, even if the labs were old and leaking! As he trained under the shortages and difficulties of war, he was able to thrive in these conditions.
Under Shinya at the University of Pennsylvania and the MBL, Ted Salmon and John Fuseler completed their PhD work. John Fuseler identified the effects of cold treatment on spindles at different stages of mitosis. Ted Salmon worked to identify the effect of pressure on the depolymerisation of the spindle. He found that as pressure increased, the spindle depolymerized. Salmon even observed chromosomal movements associated with the depolymerization. Fuseler and Salmon completed their thesis work at the MBL. Unfortunately, most biologists took many years to accept the implications of this work.