Apparatus for obtaining depth profile information from a transparent object, includes a confocal scanner for producing an en-face image of the object in an x-y plane, a spectral optical coherence tomography (OCT) apparatus for producing an OCT scan along at least one line in the z direction passing through a point in the x-y plane, and a display device. A processing unit displays on the display device the en-face image and an indication of the position of the point so as to permit the location of the OCT scan to be determined on the en-face image. The position point can be adjusted by the user when viewing the image. In other embodiments, SLO and OCT images are produced from a common aperture, and spectral OCT images are produced simultaneously with fluorescence images.