In vivo three-dimensional reconstruction of the cornea from confocal microscopy images

Confocal microscopy can provide sequences of images from all cornea layers in a rapid, in vivo and non invasive way. These images are useful to extract important clinical information on cornea state of health. We address the problem of obtaining a 3-dimensional (3D) reconstruction of the cornea starting from a confocal microscope sequence, from endothelium to epithelium. A registration procedure, based on normalized correlation, is applied to each image, because eye movements normally occur during acquisition of the sequence and shifts in x-y plane take place in the sequence of images. Information on shifts along x and y directions comes from registration process, shift along z direction comes from the instrument itself. A 2D image stack is reconstructed by taking into account shifts along x, y, and z directions. If data are missing, we reconstruct them by taking lines from adjacent images and interpolating them. After reconstruction, it is possible to display and analyze corneal structures in the 3D volume and obtain slices in the x, y, or z direction.