The densely innervated human cornea is the only superficial tissue of the human body in which nerve fibres are accessible in vivo by corneal confocal microscopy (CCM). Morphological parameters of the corneal sub-basal nerve plexus (SNP) derived from CCM images can potentially serve as a sensitive biomarker for early diagnosis of various neurodegenerative diseases. The evaluation of a single image with a typical field of view of 0.16 mm2 is insufficient for robust morphometric assessment. Mosaicking approaches have therefore been proposed to examine the SNP on a larger scale. Here we present a highly automated technique that significantly facilitates the generation of mosaic images of the SNP and is suitable for clinical tests.