A fluorescence in situ hybridization, FISH, image acquisition apparatus and a method for controlling a FISH image acquisition apparatus. A FISH probe image is acquired (S24, S44). Image processing using morphological operations is applied to identify areas of interest around locations of elevated image intensity. From this, a mask is generated (S22, S42) which filters out all but the areas of interest. The mask is applied to determine image intensity in the areas of interest. If the image intensity does not have a desired value (S26), indicating incorrect exposure of the image, then the method is repeated with one or more different exposures until an adequately exposed FISH probe image is obtained (S29, S47, S48). The correct exposure is determined either empirically by iteratively applying stepwise increases (S28), or analytically by applying a formula (S46).
