An apparatus and method for optically analyzing samples in a biological sample container containing samples arranged at different locations on the base of the container. An optical acquisition device is provided comprising a detector and an objective. The position of the upper and lower surfaces of the base at each of the sample locations is determined by a confocal polychromatic displacement sensor. Light is collected from each of the sample locations by adjusting the focal plane to be coincident with, or vertically offset from, the upper surface of the base, as determined from the displacement sensor. This allows for rapid scanning of large numbers of samples in a multi-well plate or other biological sample containers.