Theory of the Apparatus and Theory of the Phenomena: The Case of Low Dose Electron Microscopy

Abstract
In this paper 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. I extend this framework to low dose electron microscopy which has a stochastic instrument theory and which provides an exception to a thesis by Robert Ackermann on the independence between theory and instrumentation.
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