Upconversion raster scanning microscope for long-wavelength infrared imaging of breast cancer microcalcifications

This is the final version. Available from Optical Society of America via the DOI in this record. Long-wavelength identification of microcalcifications in breast cancer tissue is demonstrated using a novel upconversion raster scanning microscope. The system consists of quantum cascade lasers (QCL) for illumination and an upconversion system for efficient, high-speed detection using a silicon detector. Absorbance spectra and images of regions of ductal carcinoma in situ (DCIS) from the breast have been acquired using both upconversion and Fourier-transform infrared (FTIR) systems. The spectral images are compared and good agreement is found between the upconversion and the FTIR systems.European Unio

Pattern identification of biomedical images with time series: contrasting THz pulse imaging with DCE-MRIs

Objective We provide a survey of recent advances in biomedical image analysis and classification from emergent imaging modalities such as terahertz (THz) pulse imaging (TPI) and dynamic contrast-enhanced magnetic resonance images (DCE-MRIs) and identification of their underlining commonalities. Methods Both time and frequency domain signal pre-processing techniques are considered: noise removal, spectral analysis, principal component analysis (PCA) and wavelet transforms. Feature extraction and classification methods based on feature vectors using the above processing techniques are reviewed. A tensorial signal processing de-noising framework suitable for spatiotemporal association between features in MRI is also discussed. Validation Examples where the proposed methodologies have been successful in classifying TPIs and DCE-MRIs are discussed. Results Identifying commonalities in the structure of such heterogeneous datasets potentially leads to a unified multi-channel signal processing framework for biomedical image analysis. Conclusion The proposed complex valued classification methodology enables fusion of entire datasets from a sequence of spatial images taken at different time stamps; this is of interest from the viewpoint of inferring disease proliferation. The approach is also of interest for other emergent multi-channel biomedical imaging modalities and of relevance across the biomedical signal processing community

Scanless optical coherence tomography for high-speed 3d biomedical microscopy

Optical coherence tomography (OCT) is a high-resolution cross-sectional imaging modality that has found applications in a wide range of biomedical fields, such as ophthalmology diagnosis, interventional cardiology, surgical guidance, and oncology. OCT can be used to image dynamic scenes, in quantitative blood flow sensing and visualization, dynamic optical coherence elastography, and large-scale neural recording. However, the spatiotemporal resolution of OCT for dynamic imaging is limited by the approach it takes to scan the three-dimensional (3-D) space. In a typical OCT system, the incident light is focused to a point at the sample. The OCT system uses mechanical scanners (galvanometers or MEMS scanners) steer the probing beam to scan the transverse plane and acquires an A-scan at each transverse coordinate. For volumetric imaging, the OCT system scans individual voxels in a 3D Cartesian coordinate sequentially, resulting a limited imaging speed. In addition to limited spatiotemporal resolution, the use of mechanical scanners results in bulky sample arm and complex system configuration. This dissertation seeks to overcome limitations of conventional raster scanning approach for OCT data acquisition, by investigating novel methods to address OCT voxels in 3D space. Scanless OCT imaging is achieved through the use of spatial light modulator that precisely manipulates light wave to generate output with desired amplitude and phase. It is anticipated that the scanless OCT imaging technologies developed in this dissertation will introduce a significant paradigm shift in OCT scanning of 3D space and allow the observation of transient phenomena (neural activities, blood flow dynamics, etc.) with unprecedented spatiotemporal resolution. This research focuses on technology development and validation. Two approaches for scanless OCT imaging are investigated. One approach is optically computed optical coherence tomography (OC-OCT), and the other approach is Line field Fourier domain OCT (LF-FDOCT) based on spatial light modulator. OC-OCT takes a highly innovative optical computation strategy to extract signal from a specific depth directly without signal processing in a computer. The optical computation module in OC-OCT performs Fourier transform optically before data acquisition, by calculating the inner product between a Fourier basis function projected by the spatial light modulator and the Fourier domain interferometric signal. OC-OCT allows phase resolved volumetric OCT imaging without mechanical scanning, and has the capability to image an arbitrary 2D plane in a snapshot manner. LF-FDOCT illuminates the sample with a line field generated by a spatial light modulator. Interferometric signals from different transverse coordinates along the line field are dispersed by a grating and detected in parallel by the rows of a 2D camera. Cross-sectional image (Bscan) is obtained by performing Fourier transform along the rows of the camera. By scanning the line field electronically at the SLM, volumetric OCT imaging can be performed without mechanical scanning. In this dissertation, the principles of OC-OCT and LF-FDOCT technology are described. The imaging capability of OC-OCT and LF-FDOCT systems are quantitatively evaluated and demonstrated in 2D and 3D imaging experiments on a variety of samples

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

Diffuse Optical Biomarkers Of Breast Cancer

Diffuse optical spectroscopy/tomography (DOS/DOT) and diffuse correlation spectroscopy (DCS) employ near-infrared light to non-invasively monitor the physiology of deep tissues. These methods are well-suited to investigation of breast cancer due to their sensitivity to physiological parameters, such as hemoglobin concentration, oxygen saturation, and blood flow. This thesis utilizes these techniques to identify and develop diffuse optical biomarkers for the diagnosis and prognosis of breast cancer. Notably, a novel DOS prognostic marker for predicting pathologic complete response to neoadjuvant chemotherapy using z-score normalization and logistic regression was developed and demonstrated. This investigation found that tumors that were not hypoxic relative to the surrounding tissue were more likely to achieve complete response. Thus, the approach could enable dynamic feedback for the optimization of chemotherapy. Similar logistic regression models based on other optical parameters distinguished tumors from the surrounding normal tissue and diagnosed whether a lesion was malignant or benign. These diagnostic markers improve the ability of DOS/DOT to accurately localize tumors and could serve as a type of optical biopsy to classify suspicious lesions. Another study carried out the first longitudinal DCS blood flow monitoring over a full course of neoadjuvant chemotherapy in humans; this work explored initial correlations between blood flow and response to therapy and showed how DCS and DOS together can more accurately probe tumor physiology than either modality alone. Finally, still other thesis research included the final construction and initial imaging tests of a DOT instrument incorporated into a clinical MRI suite and the optimization of the DOT reconstruction algorithm. In total, these instrumental and algorithmic advances improved DOT image quality, helped to increase contrast between malignant and normal tissue, and eventually could lead to better understanding of tumor microvasculature. These contributions represent important steps towards the translation of diffuse optics into the clinic, demonstrating significant roles for optics to play in the diagnosis, prognosis, and physiological understanding of breast cancer

Image-Guided Raman Spectroscopic Recovery of Canine Cortical Bone Contrast in Situ

Raman scattering provides valuable biochemical and molecular markers for studying bone tissue composition with use in predicting fracture risk in osteoporosis. Raman tomography can image through a few centimeters of tissue but is limited by low spatial resolution. X-ray computed tomography (CT) imaging can provide high-resolution image-guidance of the Raman spectroscopic characterization, which enhances the quantitative recovery of the Raman signals, and this technique provides additional information to standard imaging methods. This hypothesis was tested in data measured from Teflon tissue phantoms and from a canine limb. Image-guided Raman spectroscopy (IG-RS) of the canine limb using CT images of the tissue to guide the recovery recovered a contrast of 145:1 between the cortical bone and background. Considerably less contrast was found without the CT image to guide recovery. This study presents the first known IG-RS results from tissue and indicates that intrinsically high contrasts (on the order of a hundred fold) are available

Contrast enhanced spectroscopic optical coherence tomography

A method of forming an image of a sample includes performing SOCT on a sample. The sample may include a contrast agent, which may include an absorbing agent and/or a scattering agent. A method of forming an image of tissue may include selecting a contrast agent, delivering the contrast agent to the tissue, acquiring SOCT data from the tissue, and converting the SOCT data into an image. The contributions to the SOCT data of an absorbing agent and a scattering agent in a sample may be quantified separately

Polarization-Sensitive Optical Coherence Tomography to Study Diffusion of Plasmonic Gold Nanorods- a Novel Tool for Optical Bioimaging

Optical Coherence Tomography (OCT) is an imaging tool that performs micron-resolution, non-invasive, cross-sectional imaging by measuring the echoes of backscattered light. In this thesis, a custom-designed polarization-sensitive OCT (PS-OCT) system is discussed, which is implemented in using plasmonic gold nanorods (GNRs) as diffusion probes. PS-OCT imaging is undertaken in Newtonian fluids and validation of rotational and translational diffusion of GNRs with the Stokes-Einstein relation is presented via analysis of the autocorrelations of the OCT signals. Diffusion of GNRs in non-Newtonian fluids is also studied and the frequency-dependent viscoelasticity is also explored using generalized Stokes-Einstein relation. Furthermore, diffusion of GNRs in the "correlation length >= probe" regime is discussed in low concentration polymer solutions. Biological samples such as porous extracellular matrix (ECM) and in vitro mucus are explored using PEGylated GNRs as diffusion probes with PS-OCT imaging. The diffusion of GNRs was found to be sensitive to changes in the ECM induced either by ECM-remodeling fibroblasts or by changes in the ECM concentration. In mucus, the diffusion of GNRs was observed to be slowed down by less than 7-fold compared to the solvent, suggesting that the GNRs are able to readily navigate between the mucus mesh and avoid being readily trapped, thereby illustrating the potential GNRs hold in drug-delivery across the mucus barrier to the epithelial layers in lung airways. The capability of OCT to map diffusing GNRs and speckle fluctuations resulting from other motile activities in biological samples is also presented. A longitudinal study of mammary epithelial cells cultured in 3D with fibroblasts, to study normal and pre-malignant architectural cues, carried out using the custom-designed OCT system is also presented in detail. The integration of PS-OCT imaging with the measurement of diffusing GNRs in biological samples enables OCT to perform functional imaging to supplement its excellent structural imaging capability. This thesis presents a platform for extending the reach of OCT imaging to the exciting fields of microrheology and bio-rheology, which holds tremendous promise in the assessment of micro- and nano- scale viscoelasticity of biological samples using GNRs as probes.Doctor of Philosoph