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A new, high-speed, fiber-based Mueller-matrix optical coherence tomography system with continuous source-polarization modulation is presented. For in vivo experimentation, the sample arm optics are integrated into a hand-held probe. The system’s parameters were verified through imaging standard optical elements. A unique feature of polarization-sensitive Mueller optical coherence tomography is that by measuring Jones or Mueller matrices, it can reveal the complete polarization properties of biological samples, even in the presence of diattenuation. Presented here for the first time are mapped local polarization properties of biological samples obtained by using polar decomposition in combination with least-squares fitting to differentiate measured integrated Jones matrices with respect to depth. In addition, a new concept of dual attenuation coefficients to characterize diattenuation per unit infinitesimal length in tissues is introduced. The algorithm was experimentally verified using measurements of a section of porcine tendon and the septum of a rat heart. The application of the system for burn imaging and healing monitoring was demonstrated on porcine skin because of its similarity to the human skin. The results showed a clear localization of the thermally damaged region. The local birefringence of the intravital porcine skin was mapped by using a differentiation algorithm. The burn areas in the OCT images agree well with the histology, thus demonstrating the system’s potential for burn-depth determination and post-injury healing monitoring. Another major application of the fiber-based Mueller-matrix optical coherence tomography system with continuous source-polarization modulation covered here is in vivo imaging of early stages of skin cancer. The OCT images of SENCAR mice skin affected by the tumorigenesis show the structural changes in skin resulting from precancerous papilloma formations that are consistent with histology, which proves the system’s potential for early skin cancer detection.

Optical coherence tomography (OCT) is an imaging modality analogous to ultrasound. By using the interference properties of light, one may image to micrometer resolutions using interferometric methods. Most modern systems can acquire A-scans at kHz to MHz speeds, and are capable of real-time 3D imaging. OCT has been used extensively in ophthalmology and has been used in angiography to quantify blood flow. The aim of this research has been to develop statistically optimal estimators for blood flow estimation to take advantage of these hardware advances. This is achieved through a deeper understanding of the noise characteristics of OCT. Through mathematical derivations and simulations, the noise characteristics of OCT Doppler and flow imaging were accurately modelled as additive white noise and multiplicative decorrelation noise. Decorrelation arises due to relative motion of tissue relative to the OCT region of interest and adversely affects Doppler estimation. From these models maximum likelihood estimators (MLEs) that statistically outperform the commonly used Kasai autocorrelation estimator were derived. The Cramer-Rao lower bound (CRLB), which gives the theoretical lowest estimator variance for an unbiased estimator was derived for different noise regimes. It is shown that the AWGN MLE achieves the CRLB for additive white noise dominant conditions, and the decorrelation noise MLE achieves the CRLB under more general noise conditions. The use of computational algorithms that enhance the capabilities of OCT are demonstrated. This shows that this approach for determining parametric estimators may be used in a more general medical imaging context. In addition, the use of decorrelation as a measure of speed is explored, as it is itself proportional to flow speed. / published_or_final_version / Electrical and Electronic Engineering / Doctoral / Doctor of Philosophy

Optical coherence tomography (OCT), as a newly developed imaging modality, has attracted significant attention due to its capability to obtain the cross-sectional information of biological tissues in a non-invasive way, with resolution in the range of several micrometers. The third-generation swept source OCT (SS-OCT), is superior in the speed, imaging range and signal-to-noise ratio (SNR) compared with the previous time-domain OCT (TD-OCT) and spectral domain OCT (SD-OCT), and therefore forms our research focus. In this thesis, for the first time, I investigate the deployment of Fourier domain mode-locked (FDML) swept laser by utilizing the bismuth-based erbium doper fiber (Bi-EDF) with a sweeping bandwidth of ~ 81nm achieved. Following, fiber Raman amplifier (FRA) is also investigated by employing multiple Raman pumps. The tuning range is ~111.8nm, which is much larger than the previous reported Raman pumped FDML in the 1550nm region. Imaging was performed to validate the feasibility of the proposed schemes for the SS-OCT applications, respectively. In addition to the FDML swept laser cavity design, speckle noise reduction is also of great importance in OCT, which can significantly improve the visibility of the obtained OCT images. I demonstrate two different speckle reduction methods for OCT applications, which are superior in suppressing speckle noise and reserving the one-dimensional (1D) and two-dimensional (2D) signal information, respectively. Applying the proposed wavelet domain compounding (WDC) and contourlet shrinkage method to despeckle the OCT images, the visibility of the OCT images was significantly improved, with negligible edge preservation compromise. Spectroscopic information is also of interest to many researchers as it provides additional spectroscopic contrast, which on one hand, will improve the visualization of the images, and on the other hand, will enable the classification of different tissue types and help the process of discrimination between invasive and noninvasive tumors. Compared with our previous reported work about dual-band spectroscopic OCT based on optical parametric amplifier (OPA) to generate another idler band, which will be used as the second band for dual-band spectroscopic analysis, I further extend the dual-band spectroscopic OCT to the endoscopic applications, and investigate the dual-band FDML swept laser configuration based on a custom-designed dual-channel driver to synchronize the two different wavelength bands, centered at 1310 and 1550 nm, respectively. OCT Images for different bands are captured and post-processed by coding the spectral difference in different colors. In short, in this thesis, the investigations of OCT range from system design, speckle reduction to the spectroscopic applications. All these research efforts will extend the current FDML techniques for a wide range of SS-OCT applications. These schemes may be useful in OCT swept laser source build up, speckle noise reduction, and the extension of spectroscopic analysis. / published_or_final_version / Electrical and Electronic Engineering / Doctoral / Doctor of Philosophy

The development of two different classes of optical sources for TD-OCT and FD-OCT are presented in this thesis. The design of several low-cost, high-performance BBSs, based on the ASE of two SOAs and EDF, are presented. Two different configuration types that were designed in this thesis are found to be effective BBSs. These sources are implemented in a TD-OCT system and therefore imaging performance is discussed as well. Secondly, two different WSSs based on mode-locked SFRLs with applications in SS-OCT are presented. / From our experimental results with BBSs, we conclude that: (1) S/C-band output produced by the ASE emitted from two cascaded SOAs can be effectively extended with L-band output produced from the ASE of EDF; (2) An even broader output is achievable by: coupling the C-band and L-band outputs from a C-band SOA and EDF respectively and then amplifying the coupled output through an S-band SOA; (3) OCT imaging systems employing a light source with an S+C+L band output, with a center wavelength of approximately 1520 nm, can achieve high penetration depths in biological tissue. / From our experimental results with SFRLs, we conclude that: (1) Our two SFRL configurations generate picosecond pulses with reasonably narrow linewidths: 0.2--0.5 nm, and a sweeping range of about 50 nm; (2) These SFRLs can function as laser swept sources by setting the driving frequency of the RF generator to a periodic ramping function.

Thesis (Ph. D.)--University of Iowa, 2008. / Thesis supervisor: Milan Sonka. Includes bibliographical references (leaves 145-150).

Thesis (Ph. D.)--University of Iowa, 2009. / Thesis supervisors: Sonka, Michael D. Abràmoff. Includes bibliographical references (leaves 76-80).

Thesis (M.S.)--Marquette University, 2009. / Access available to Marquette University only. Joseph Carroll, Kristina Ropella, Taly Gilat-Schmidt, Advisors.

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