Electron microscopy, and in particular low dose electron microscopy, offers interesting cases of experimental techniques where the theory of the phenomena studied and the theory of the apparatus used, are intertwined. A single primary exposure usually does not give an interpretable image, and computerized image enhancement techniques are used to create from multiple exposures a single, visually meaningful image. Some of the enhancement programs start from informed guesses at the structure of the specimen and use the primary exposures in a series of corrections to arrive at a image that can be read by trained observers.
In this paper I describe in the general deterministic case the possible relations between phenomena theory and instrument theory. I give a Bayesian criterion for when an experiment is a test of the theory of the apparatus, rather than a test of the theory of the phenomena, and describe strategies used to ensure that tests of the theory of the phenomena are possible.