No special effects are used. The "superimpositions" are captured reflections and the prismatic effects are due to the hand-rolled glass in the windows of the train.
Stan Brakhage was paid $200 to document the 3rd Ave. El (train) in New York City. Thatfootage became this film.
This film is included on "By Brakhage: an Anthology", which is part of the Criterion Collection, spine #184.