Improved adaptive complex diffusion despeckling filter

Despeckling optical coherence tomograms from the human retina is a fundamental step to a better diagnosis or as a preprocessing stage for retinal layer segmentation. Both of these applications are particularly important in monitoring the progression of retinal disorders. In this study we propose a new formulation for a well-known nonlinear complex diffusion filter. A regularization factor is now made to be dependent on data, and the process itself is now an adaptive one. Experimental results making use of synthetic data show the good performance of the proposed formulation by achieving better quantitative results and increasing computation speed.Fundação para a Ciência e TecnologiaFEDERPrograma COMPET

Automated quantification and classification of human kidney microstructures obtained by optical coherence tomography

Optical coherence tomography (OCT) is a rapidly emerging imaging modality that can non-invasively provide cross-sectional, high-resolution images of tissue morphology such as kidney in situ and in real-time. Because the viability of a donor kidney is closely correlated with its tubular morphology, and a large amount of image datasets are expected when using OCT to scan the entire kidney, it is necessary to develop automated image analysis methods to quantify the spatially-resolved morphometric parameters such as tubular diameter, and to classify various microstructures. In this study, we imaged the human kidney in vitro, quantified the diameters of hollow structures such as blood vessels and uriniferous tubules, and classified those structures automatically. The quantification accuracy was validated. This work can enable studies to determine the clinical utility of OCT for kidney imaging, as well as studies to evaluate kidney morphology as a biomarker for assessing kidney's viability prior to transplantation

2D Fourier Fractal Analysis of Optical Coherence Tomography Images of Basal Cell Carcinomas and Melanomas

The optical coherence tomography (OCT) technique is applied in the diagnosis of the skin tissue. In general, quantitative imaging features obtained from OCT images have already been used as biomarkers to categorize skin tumors. Particularly, the fractal dimension (FD) could be capable of providing an efficient approach for analyzing OCT images of skin tumors. The 2D Fourier fractal analysis (FFA) as well as the differential box counting method (DBCM) was used in this paper to classify the basal cell carcinomas (BCC), melanomas, and benign melanocytic nevi. Generalized estimating equations were used to test for differences between skin tumors. Our results showed that the significant decrease of the 2D FD was detected in the benign melanocytic nevi and basal cell carcinomas as compared with the melanomas. Our results also suggested that the 2D FFA could provide a more efficient way to calculating FD to differentiate the basal cell carcinomas, melanomas, and benign melanocytic nevi as compared to the 2D DBCM

Back to Basics: Fast Denoising Iterative Algorithm

We introduce Back to Basics (BTB), a fast iterative algorithm for noise reduction. Our method is computationally efficient, does not require training or ground truth data, and can be applied in the presence of independent noise, as well as correlated (coherent) noise, where the noise level is unknown. We examine three study cases: natural image denoising in the presence of additive white Gaussian noise, Poisson-distributed image denoising, and speckle suppression in optical coherence tomography (OCT). Experimental results demonstrate that the proposed approach can effectively improve image quality, in challenging noise settings. Theoretical guarantees are provided for convergence stability

NONINVASIVE MULTIMODAL DIFFUSE OPTICAL IMAGING OF VULNERABLE TISSUE HEMODYNAMICS

Measurement of tissue hemodynamics provides vital information for the assessment of tissue viability. This thesis reports three noninvasive near-infrared diffuse optical systems for spectroscopic measurements and tomographic imaging of tissue hemodynamics in vulnerable tissues with the goal of disease diagnosis and treatment monitoring. A hybrid near-infrared spectroscopy/diffuse correlation spectroscopy (NIRS/DCS) instrument with a contact fiber-optic probe was developed and utilized for simultaneous and continuous monitoring of blood flow (BF), blood oxygenation, and oxidative metabolism in exercising gastrocnemius. Results measured by the hybrid NIRS/DCS instrument in 37 subjects (mean age: 67 ± 6) indicated that vitamin D supplement plus aerobic training improved muscle metabolic function in older population. To reduce the interference and potential infection risk on vulnerable tissues caused by the contact measurement, a noncontact diffuse correlation spectroscopy/tomography (ncDCS/ncDCT) system was then developed. The ncDCS/ncDCT system employed optical lenses to project limited numbers of sources and detectors on the tissue surface. A motor-driven noncontact probe scanned over a region of interest to collect boundary data for three dimensional (3D) tomographic imaging of blood flow distribution. The ncDCS was tested for BF measurements in mastectomy skin flaps. Nineteen (19) patients underwent mastectomy and implant-based breast reconstruction were measured before and immediately after mastectomy. The BF index after mastectomy in each patient was normalized to its baseline value before surgery to get relative BF (rBF). Since rBF values in the patients with necrosis (n = 4) were significantly lower than those without necrosis (n = 15), rBF levels can be used to predict mastectomy skin flap necrosis. The ncDCT was tested for 3D imaging of BF distributions in chronic wounds of 5 patients. Spatial variations in BF contrasts over the wounded tissues were observed, indicating the capability of ncDCT in detecting tissue hemodynamic heterogeneities. To improve temporal/spatial resolution and avoid motion artifacts due to a long mechanical scanning of ncDCT, an electron-multiplying charge-coupled device based noncontact speckle contrast diffuse correlation tomography (scDCT) was developed. Validation of scDCT was done by imaging both high and low BF contrasts in tissue-like phantoms and human forearms. In a wound imaging study using scDCT, significant lower BF values were observed in the burned areas/volumes compared to surrounding normal tissues in two patients with burn. One limitation in this study was the potential influence of other unknown tissue optical properties such as tissue absorption coefficient (µa) on BF measurements. A new algorithm was then developed to extract both µa and BF using light intensities and speckle contrasts measured by scDCT at multiple source-detector distances. The new algorithm was validated using tissue-like liquid phantoms with varied values of µa and BF index. In-vivo validation and application of the innovative scDCT technique with the new algorithm is the subject of future work

Dual modality optical coherence tomography : Technology development and biomedical applications

Optical coherence tomography (OCT) is a cross-sectional imaging modality that is widely used in clinical ophthalmology and interventional cardiology. It is highly promising for in situ characterization of tumor tissues. OCT has high spatial resolution and high imaging speed to assist clinical decision making in real-time. OCT can be used in both structural imaging and mechanical characterization. Malignant tumor tissue alters morphology. Additionally, structural OCT imaging has limited tissue differentiation capability because of the complex and noisy nature of the OCT signal. Moreover, the contrast of structural OCT signal derived from tissue’s light scattering properties has little chemical specificity. Hence, interrogating additional tissue properties using OCT would improve the outcome of OCT’s clinical applications. In addition to morphological difference, pathological tissue such as cancer breast tissue usually possesses higher stiffness compared to the normal healthy tissue, which indicates a compelling reason for the specific combination of structural OCT imaging with stiffness assessment in the development of dual-modality OCT system for the characterization of the breast cancer diagnosis. This dissertation seeks to integrate the structural OCT imaging and the optical coherence elastography (OCE) for breast cancer tissue characterization. OCE is a functional extension of OCT. OCE measures the mechanical response (deformation, resonant frequency, elastic wave propagation) of biological tissues under external or internal mechanical stimulation and extracts the mechanical properties of tissue related to its pathological and physiological processes. Conventional OCE techniques (i.e., compression, surface acoustic wave, magnetomotive OCE) measure the strain field and the results of OCE measurement are different under different loading conditions. Inconsistency is observed between OCE characterization results from different measurement sessions. Therefore, a robust mechanical characterization is required for force/stress quantification. A quantitative optical coherence elastography (qOCE) that tracks both force and displacement is proposed and developed at NJIT. qOCE instrument is based on a fiber optic probe integrated with a Fabry-Perot force sensor and the miniature probe can be delivered to arbitrary locations within animal or human body. In this dissertation, the principle of qOCE technology is described. Experimental results are acquired to demonstrate the capability of qOCE in characterizing the elasticity of biological tissue. Moreover, a handheld optical instrument is developed to allow in vivo real-time OCE characterization based on an adaptive Doppler analysis algorithm to accurately track the motion of sample under compression. For the development of the dual modality OCT system, the structural OCT images exhibit additive and multiplicative noises that degrade the image quality. To suppress noise in OCT imaging, a noise adaptive wavelet thresholding (NAWT) algorithm is developed to remove the speckle noise in OCT images. NAWT algorithm characterizes the speckle noise in the wavelet domain adaptively and removes the speckle noise while preserving the sample structure. Furthermore, a novel denoising algorithm is also developed that adaptively eliminates the additive noise from the complex OCT using Doppler variation analysis

Optical and material properties of varnishes for paintings

Clear varnish coatings are applied to the surface of historic paintings to provide a protective barrier layer and/or change their appearance. The natural varnishes used by the original artist would have given the painting its original finished appearance. Over a period of years these varnish layers degrade with age, which changes the appearance. Then it becomes necessary to remove and replace the coating. This removal and replacement is undesirable as it can lead to damage of the painting. Synthetic alternatives can provide a much longer life coating but may not give the same appearance. This thesis details research into the soft matter physics and fluid mechanisms that determine the relationships between the material properties of varnishes and their effect on the appearance of paintings