Optical coherence tomography (OCT) provides the axial profile of back-scattered light from biological tissues and enables non-invasive, three-dimensional structure imaging. Since the introduction of OCT technique, OCT has shown its powerful utility especially in the field of ophthalmology. However its capability is still limited to the structural investigation. Because many eye diseases are tightly associated with tissue functions such as blood circulation and tissue microstructure, development of functional OCT is important. Since the necessity of functional extension of OCT technique got more attention, Doppler OCT and polarization-sensitive OCT (PS-OCT) have been developed for blood flow and birefringence measurements, respectively, and have been widely utilized for ophthalmic imaging for clinical and pathological research purposes. Jones-matrix-based OCT, also named as Jones matrix tomography (JMT), was originally designed as one type of PS-OCTs capable of measuring the polarization properties of biological tissue. In this dissertation, an advance version of JMT system is developed and also novel applications of JMT in ophthalmology is introduced.

New JMT algorithms are developed, which make JMT system being capable of multi-contrast imaging including scattering, localized flow, and polarization contrasts. Novel spectral shift compensation and adaptive averaging methods are devised for achieving sensitivity-enhanced scattering OCT and polarization property measurements. Especially, by stabilizing the phase of the system, Doppler flow measurement is achieved with a high sensitivity.

As a new clinical application, JMT is utilized for three-dimensional volumetric in vivo imaging of human eyelid. With the degree of polarization uniformity contrast (DOPU), one of the polarization contrasts produced by JMT, meibomian glands (MGs) are exclusively segmented from OCT volumetric image. With MG segmentation, its age-dependent morphological characteristics are further investigated.

As another clinical application, JMT is also utilized for investigating corneal collagen cross-linking (CXL) effect on cornea stroma. Fresh bovine corneas are treated by two different CXL protocols (standard and accelerated CXL) and measured ex vivo. Morphological changes on the cornea after the two different protocols are cross-examined to evaluate their treatment outcomes in terms of the cross-linking effectiveness and progression.

Through this study, JMT is shown to have great potential to monitor and diagnose many different ocular diseases non-invasively.