Over the past several years, optical coherence tomography (OCT) has evolved into a powerful tool for the in vivo investigation of cross-sectional retinal anatomy and pathology.^1,2 OCT extracts depth-resolved information about the intensity of backscattered light from retinal layers using low coherence interferometry. The amount of light backscattered/reflected from the retinal layers can provide critical information regarding tissue properties and underlying changes. Furthermore, measuring changes in the angular (directional) scattering of retina layers might further enhance our ability to sense microscopic changes in cellular and subcellular morphology that might precede and/or follow disease progression. However, this information is not utilized in current clinical OCT systems. The reduction in light scattered by the retinal nerve fiber layer (RFNL) near the optic nerve head is reported to be an early indicator of axonal degeneration and a sensitive way to detect glaucomatous damage.^{3 – 5} The reflection from the RFNL is found to be highly directional, and the implications of the variability caused by the directional reflectance on clinical measurements are reported.⁶ The directional scattering properties exhibited by the Henle’s fiber layer (HFL) in human retina account for their oblique orientation with respect to the outer nuclear layer (ONL). Therefore, directional OCT (dOCT) imaging of human retina enables the delineation of HFL from the ONL and accurate measurement of macular photoreceptor nuclear layer thickness, which are important biomarkers for retinal degenerations.^7,8 The directional reflectance property shown by the photoreceptor bands, known as the optical Stiles–Crawford effect (SCE), provides the information on the structural integrity of the photoreceptors. An OCT-based assessment of the reflectivity of the photoreceptors layer is reported to study SCE in human retina.⁹

The retina is a visually accessible portion of the central nervous system situated at the focal plane of a natural optical system and therefore affords a unique opportunity for noninvasively visualizing the changes associated with neurodegenerative disorders and vascular alterations of neural tissue.^1,2 Recent progress in high-resolution retinal imaging has achieved sufficient resolution and sensitivity to take full advantage of this opportunity in humans.³ The opportunity also applies to the mouse, a primary animal model for studying human biology and disease.⁴ Mouse models are important not only in basic vision science and ophthalmic research,⁵ including studies of the mechanism of phototransduction,^6,7 but also in general neuroscience.⁸ Interestingly, the special optical features of the mouse eye, which has a numerical aperture (NA) twice than that of the human eye,⁹ offer a potentially higher resolution for retinal imaging.¹⁰ However, the retinal neurons anterior to photoreceptors—i.e., bipolar, horizontal, amacrine, or ganglion cells (GCs)—are nearly transparent, making them very difficult to image in the living eye using imaging modalities employing only label-free backscattered light.

The automatic calibration in Fourier-domain optical coherence tomography (FD-OCT) systems allows for high resolution imaging with precise depth ranging functionality in many complex imaging scenarios, such as microsurgery. However, the accuracy and speed of the existing automatic schemes are limited due to the functional approximations and iterative operations used in their procedures. In this paper, we present a new real-time automatic calibration scheme for swept source-based optical coherence tomography (SS-OCT) systems. The proposed automatic calibration can be performed during scanning operation and does not require an auxiliary interferometer for calibration signal generation and an additional channel for its acquisition. The proposed method makes use of the spectral component corresponding to the sample surface reflection as the calibration signal. The spectral phase function representing the non-linear sweeping characteristic of the frequency-swept laser source is determined from the calibration signal. The phase linearization with improved accuracy is achieved by normalization and rescaling of the obtained phase function. The fractional-time indices corresponding to the equidistantly spaced phase intervals are estimated directly from the resampling function and are used to resample the OCT signals. The proposed approach allows for precise calibration irrespective of the path length variation induced by the non-planar topography of the sample or galvo scanning. The conceived idea was illustrated using an in-house-developed SS-OCT system by considering the specular reflection from a mirror and other test samples. It was shown that the proposed method provides high-performance calibration in terms of axial resolution and sensitivity without increasing computational and hardware complexity.

This letter reports an efficient phase analysis-based direct time domain resampling scheme for swept source-based optical coherence tomography (SS-OCT) systems. The unwrapped phase values, representing non-linear frequency sweeping of the laser, are extracted from the calibration signal generated by a Mach–Zehnder interferometer. Equidistant wavenumber spaces are calculated by normalizing obtained phase values followed by scaling to the maximum number of sampling points. The non-uniform fractional time index values corresponding to the uniformly distributed phase values are computed directly from the linearizer coordinates in order to eliminate the use of the polynomial fitting approach that is used in existing phase-based time domain resampling methods. This proposed linearization scheme shows a significant improvement in performance in terms of accuracy and speed in comparison with the major existing schemes. The robustness of the algorithm, as well as its impact on the resolution and sensitivity, are illustrated using an in-house-developed SS-OCT system and by performing imaging of a human finger nail and an eye model as test samples.

For in vivo mouse retinal imaging, especially with Adaptive Optics instruments, application of a contact lens is desirable, as it allows maintenance of cornea hydration and helps to prevent cataract formation during lengthy imaging sessions. However, since the refractive elements of the eye (cornea and lens) serve as the objective for most in vivo retinal imaging systems, the use of a contact lens, even with 0 Dpt. refractive power, can alter the system's optical properties. In this investigation we examined the effective focal length change and the aberrations that arise from use of a contact lens. First, focal length changes were simulated with a Zemax mouse eye model. Then ocular aberrations with and without a 0 Dpt. contact lens were measured with a Shack-Hartmann wavefront sensor (SHWS) in a customized AO-SLO system. Total RMS wavefront errors were measured for two groups of mice (14-month, and 2.5-month-old), decomposed into 66 Zernike aberration terms, and compared. These data revealed that vertical coma and spherical aberrations were increased with use of a contact lens in our system. Based on the ocular wavefront data we evaluated the effect of the contact lens on the imaging system performance as a function of the pupil size. Both RMS error and Strehl ratios were quantified for the two groups of mice, with and without contact lenses, and for different input beam sizes. These results provide information for determining optimum pupil size for retinal imaging without adaptive optics, and raise critical issues for design of mouse optical imaging systems that incorporate contact lenses.