Dopant fluctuations and other defects in silicon wafers can lead to systematic errors in several parameters in particle or single-photon detection. In imaging applications non-uniformities in sensors or readout give rise to fixed pattern image noise and degradation of achievable spatial resolution for a given flux. High granularity pixel detectors offer the possibility to investigate local properties of the detector material on a microscopic scale. In this paper, we study fixed pattern detection fluctuations and detector inhomogeneities using the Medipix1 readout chip. Low-frequency fixed pattern signal deviations due to dopant inhomogeneities can be separated from high-frequency deviations.