New technologies for optical coherence microscopy

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.Includes bibliographical references.According to the American Cancer Society, gastrointestinal (GI) cancers are among the most common forms of malignancies suffered today, affecting -200,000 people and causing -80,000 deaths in the United States every year. The prognosis depends heavily on the detection of early-stage lesions. The process of endoscopic surveillance, excisional biopsy, and histologic examination is the current gold standard for screening and diagnosis of many GI cancers. This process, however, is invasive, time-consuming, and can suffer from unacceptable false negative rates. Optical imaging technology that provides real-time, high-resolution imaging of human tissue in vivo with resolution at or near that of histopathology may significantly improve clinicians' capabilities to identify malignancies at curable stages. The ability to assess histologic hallmarks of GI cancer at the tissue architectural and cellular levels without excisional biopsy would be a major advance in GI cancer management. Development of techniques to reliably image cellular and subcellular structure through endoscopic devices is one of the most outstanding challenges in biomedical imaging today and holds tremendous promise for surgical applications and for early diagnostic screening and staging of epithelial malignancies. Optical coherence microscopy (OCM) is an in vivo cellular imaging technique that combines OCT with confocal microscopy. Due to the unique feature of using two distinct optical sectioning techniques, OCM can provide superior imaging depth in highly scattered tissues and can overcome important imaging probe design limitations that hinder confocal microscopy. Two novel designs for OCM systems are proposed and developed for high resolution cellular imaging. The first uses Fourier domain optical coherence detection, and the second implements line-field illumination and detection. Differences in performance from the standard time-domain optical coherence microscopy systems will be studied.by Shu-Wei Huang.S.M

Endoscopic optical coherence tomography for clinical studies in the gastrointestinal tract

Thesis (Ph. D.)--Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2013.Cataloged from PDF version of thesis.Includes bibliographical references.Optical coherence tomography (OCT) performs micrometer-scale, cross-sectional and three dimensional imaging by measuring the echo time delay of backscattered light. OCT imaging is performed using low-coherence interferometry. With the development of Fourier domain detection techniques and fiber-optic based OCT endoscopes, high speed internal body imaging was enabled, which makes OCT suitable for clinical research in the human gastrointestinal (GI) tract. Endoscopic OCT imaging is challenging because fast and stable optical scanning must be implemented inside a small imaging probe to acquire useable volumetric information from internal human bodies. Although several studies have shown the use of endoscopic OCT in human gastrointestinal tracts as a real-time surveillance tool, the capability of OCT has not yet been fully explored in endoscopic applications and OCT is not well accepted as a standard imaging modality for GI clinics due to hardware limitations and lack of comprehensive clinical evidences. This thesis presents a number of clinical studies using endoscopic OCT that provide solutions to clinical problems in the GI tract supported by statistically significant results and the development of ultrahigh speed endoscopic OCT system that enables advanced OCT imaging applications. In collaboration with medical partners, the structural features in the diseased esophagus identified from OCT images are compared before and immediately after different ablative therapies, and features that predict the treatment response are investigated. Working in collaboration with industrial partners, an ultrahigh speed endoscopic OCT imaging system is constructed for clinical research in gastroenterology. Distally actuated imaging catheters are developed, enabling the visualization of the detailed three-dimensional (3D) structure in the gastrointestinal tract. Finally, clinical pilot studies are conducted and demonstrate the utility of the ultrahigh speed endoscopic OCT imaging for broader surveillance coverage, pathology detection, and dye-less contrast enhancement. The convergence of 3D spatial resolution, imaging speed, field of view, and minimally invasive access enabled by endoscopic OCT are unmatched by most other biomedical imaging techniques. Though still in its early stage of clinical validation, endoscopic OCT may have a profound impact on human healthcare and industrial inspection by enabling visualization and quantification of 3D microstructure in situ and in real time.by Tsung-Han Tsai.Ph.D

TOWARDS HIGH RESOLUTION ENDOSCOPIC OPTICAL COHERENCE TOMOGRAPHY FOR IMAGING INTERNAL ORGANS

Optical coherence tomography (OCT) is a light based interferometric imaging technique that can provide high resolution (5-20 µm at 1300 nm), depth resolved, images in real-time. With recent advances in portable low coherent light sources for OCT it is now possible to achieve ultrahigh axial resolutions (≤ 3 µm) by moving to shorter central wavelengths such as 800 nm while utilizing a broad spectral bandwidth. Our goal was to push ultrahigh resolution OCT technology to in vivo imaging of internal organs for endoscopic assessment of tissue microstructure. This dissertation is separated into technological developments and biomedical imaging studies. Technological developments in this dissertation included development of a high speed, ultrahigh resolution distal scanning catheter. This catheter was based upon a miniature DC micromotor capable of rotational velocities in excess of 100 rps, a diffractive compound lens design that minimized chromatic aberrations, and a mechanical assembly that limited field of view blockage to less than 7.5% and maintained an outer diameter of 1.78 mm (with plastic sheath). In conjunction with the algorithm described in chapter 4 to correct for non-uniform rotational distortion, the overall imaging system was capable of high quality endoscopic imaging of internal organs in vivo. Equipped with the ultrahigh resolution endoscopic OCT system, imaging was performed in small airways and colorectal cancer. Imaging results demonstrated the ability to directly visualization of microstructural details such as airway smooth muscle in the small airways representing a major step forward in pulmonary imaging. With the ability to visualize airway smooth muscle, morphological changes in COPD and related diseases can be further investigated. Additionally, longitudinal changes in an ETBF induced colon cancer model in APCMin mice were studied as well. Quantitative assessment of tissue microarchitecture was performed by measuring the attenuation coefficient to find a bimodal distribution separating normal healthy tissue from polyps. Finally, results from two additional projects were also demonstrated. Chapter 7 shows some results from vascular imaging in a tumor angiogenesis model and middle cerebral artery occlusion model. Chapter 8 describes an endoscopic multimodal OCT and fluorescence imaging platform with results in ex vivo rabbit esophagus

Low-cost portable microscopy systems for biomedical imaging and healthcare applications

In recent years, the development of low-cost portable microscopes (LPMs) has opened new possibilities for disease detection and biomedical research, especially in resource-limited areas. Despite these advancements, the majority of existing LPMs are hampered by sophisticated optical and mechanical designs, require extensive post-data analysis, and are often tailored for specific biomedical applications, limiting their broader utility. Furthermore, creating an optical-sectioning microscope that is both compact and cost effective presents a significant challenge. Addressing these critical gaps, this PhD study aims to: (1) develop a universally applicable LPM featuring a simplified mechanical and optical design for real-time biomedical imaging analysis, and (2) design a novel, smartphone-based optical sectioning microscope that is both compact and affordable. These objectives are driven by the need to enhance accessibility to quality diagnostic tools in varied settings, promising a significant leap forward in the democratization of biomedical imaging technologies. With 3D printing, optimised optical design, and AI techniques, we can develop LPM’s real time analysis functionality. I conducted a literature review on LPMs and related applications in my study and implemented two low-cost prototype microscopes and one theoretical study. 1) The first project is a portable AI fluorescence microscope based on a webcam and the NVIDIA Jetson Nano (NJN) with real-time analysis functionality. The system was 3D printed, weighing ~250 grams with a size of 145mm × 172 mm × 144 mm (L×W×H) and costing ~$400. It achieves a physical magnification of ×5 and can resolve 228.1 lp/mm USAF features. The system can recognise and count fluorescent beads and human red blood cells (RBCs). 2) I developed a smartphone-based optical sectioning microscope using the HiLo technique. To our knowledge, it is the first smartphone-based HiLo microscope that offers low-cost optical-sectioned widefield imaging. It has a 571.5 μm telecentric scanning range and an 11.7 μm axial resolution. I successfully used it to realize optical sectioning imaging of fluorescent beads. For this system, I developed a new low-cost HiLo microscopy technique using microlens arrays (MLAs) with incoherent light-emitting diode (LED) light sources. I conducted a numerical simulation study assessing the integration of uncoherent LEDs and MLAs for a low-cost HiLo system. The MLA can generate structured illumination in HiLo. How the MLA’s geometry structure and physical parameters affect the image performance were discussed in detail. This PhD thesis explores the advancement of low-cost portable microscopes (LPMs) through the integration of 3D printing, optimized optical design, and artificial intelligence (AI) techniques to enhance their real-time analysis capabilities. The research involved a comprehensive literature review on LPMs and their applications, leading to the development of two innovative prototype LPMs, alongside a theoretical study. These works contribute significantly to the field by not only addressing the technical and financial barriers associated with advanced microscopy but also by laying the groundwork for future innovations in portable and accessible biomedical imaging. Through its focus on simplification, affordability, and practicality, the research holds promise for substantially expanding the reach and impact of diagnostic imaging technologies, especially in those resource-limited areas.In recent years, the development of low-cost portable microscopes (LPMs) has opened new possibilities for disease detection and biomedical research, especially in resource-limited areas. Despite these advancements, the majority of existing LPMs are hampered by sophisticated optical and mechanical designs, require extensive post-data analysis, and are often tailored for specific biomedical applications, limiting their broader utility. Furthermore, creating an optical-sectioning microscope that is both compact and cost effective presents a significant challenge. Addressing these critical gaps, this PhD study aims to: (1) develop a universally applicable LPM featuring a simplified mechanical and optical design for real-time biomedical imaging analysis, and (2) design a novel, smartphone-based optical sectioning microscope that is both compact and affordable. These objectives are driven by the need to enhance accessibility to quality diagnostic tools in varied settings, promising a significant leap forward in the democratization of biomedical imaging technologies. With 3D printing, optimised optical design, and AI techniques, we can develop LPM’s real time analysis functionality. I conducted a literature review on LPMs and related applications in my study and implemented two low-cost prototype microscopes and one theoretical study. 1) The first project is a portable AI fluorescence microscope based on a webcam and the NVIDIA Jetson Nano (NJN) with real-time analysis functionality. The system was 3D printed, weighing ~250 grams with a size of 145mm × 172 mm × 144 mm (L×W×H) and costing ~$400. It achieves a physical magnification of ×5 and can resolve 228.1 lp/mm USAF features. The system can recognise and count fluorescent beads and human red blood cells (RBCs). 2) I developed a smartphone-based optical sectioning microscope using the HiLo technique. To our knowledge, it is the first smartphone-based HiLo microscope that offers low-cost optical-sectioned widefield imaging. It has a 571.5 μm telecentric scanning range and an 11.7 μm axial resolution. I successfully used it to realize optical sectioning imaging of fluorescent beads. For this system, I developed a new low-cost HiLo microscopy technique using microlens arrays (MLAs) with incoherent light-emitting diode (LED) light sources. I conducted a numerical simulation study assessing the integration of uncoherent LEDs and MLAs for a low-cost HiLo system. The MLA can generate structured illumination in HiLo. How the MLA’s geometry structure and physical parameters affect the image performance were discussed in detail. This PhD thesis explores the advancement of low-cost portable microscopes (LPMs) through the integration of 3D printing, optimized optical design, and artificial intelligence (AI) techniques to enhance their real-time analysis capabilities. The research involved a comprehensive literature review on LPMs and their applications, leading to the development of two innovative prototype LPMs, alongside a theoretical study. These works contribute significantly to the field by not only addressing the technical and financial barriers associated with advanced microscopy but also by laying the groundwork for future innovations in portable and accessible biomedical imaging. Through its focus on simplification, affordability, and practicality, the research holds promise for substantially expanding the reach and impact of diagnostic imaging technologies, especially in those resource-limited areas

NOVEL TECHNOLOGIES AND APPLICATIONS FOR FLUORESCENT LAMINAR OPTICAL TOMOGRAPHY

Laminar optical tomography (LOT) is a mesoscopic three-dimensional (3D) optical imaging technique that can achieve both a resolution of 100-200 µm and a penetration depth of 2-3 mm based either on absorption or fluorescence contrast. Fluorescence laminar optical tomography (FLOT) can also provide large field-of-view (FOV) and high acquisition speed. All of these advantages make FLOT suitable for 3D depth-resolved imaging in tissue engineering, neuroscience, and oncology. In this study, by incorporating the high-dynamic-range (HDR) method widely used in digital cameras, we presented the HDR-FLOT. HDR-FLOT can moderate the limited dynamic range of the charge-coupled device-based system in FLOT and thus increase penetration depth and improve the ability to image fluorescent samples with a large concentration difference. For functional mapping of brain activities, we applied FLOT to record 3D neural activities evoked in the whisker system of mice by deflection of a single whisker in vivo. We utilized FLOT to investigate the cell viability, migration, and bone mineralization within bone tissue engineering scaffolds in situ, which allows depth-resolved molecular characterization of engineered tissues in 3D. Moreover, we investigated the feasibility of the multi-modal optical imaging approach including high-resolution optical coherence tomography (OCT) and high-sensitivity FLOT for structural and molecular imaging of colon tumors, which has demonstrated more accurate diagnosis with 88.23% (82.35%) for sensitivity (specificity) compared to either modality alone. We further applied the multi-modal imaging system to monitor the drug distribution and therapeutic effects during and after Photo-immunotherapy (PIT) in situ and in vivo, which is a novel low-side-effect targeted cancer therapy. A minimally-invasive two-channel fluorescence fiber bundle imaging system and a two-photon microscopy system combined with a micro-prism were also developed to verify the results

Extended field-of-view ultrathin microendoscopes with built-in aberration correction for high-resolution functional imaging with minimal invasiveness

TB

Biomedical Photoacoustic Imaging and Sensing Using Affordable Resources

The overarching goal of this book is to provide a current picture of the latest developments in the capabilities of biomedical photoacoustic imaging and sensing in an affordable setting, such as advances in the technology involving light sources, and delivery, acoustic detection, and image reconstruction and processing algorithms. This book includes 14 chapters from globally prominent researchers , covering a comprehensive spectrum of photoacoustic imaging topics from technology developments and novel imaging methods to preclinical and clinical studies, predominantly in a cost-effective setting. Affordability is undoubtedly an important factor to be considered in the following years to help translate photoacoustic imaging to clinics around the globe. This first-ever book focused on biomedical photoacoustic imaging and sensing using affordable resources is thus timely, especially considering the fact that this technique is facing an exciting transition from benchtop to bedside. Given its scope, the book will appeal to scientists and engineers in academia and industry, as well as medical experts interested in the clinical applications of photoacoustic imaging

Photoacoustic imaging of colorectal cancer and ovarian cancer

Photoacoustic (PA) imaging is an emerging hybrid imaging technology that uses a short-pulsed laser to excite tissue. The resulting photoacoustic waves are used to image the optical absorption distribution of the tissue, which is directly related to micro-vessel networks and thus to tumor angiogenesis, a key process in tumor growth and metastasis. In this thesis, the acoustic-resolution photoacoustic microscopy (AR-PAM) was first investigated on its role in human colorectal tissue imaging, and the optical-resolution photoacoustic microscopy (OR-PAM) was investigated on its role in human ovarian tissue imaging.Colorectal cancer is the second leading cause of cancer death in the United States. Significant limitations in screening and surveillance modalities continue to hamper early detection of primary cancers or recurrences after therapy. In the first phase of the study, benchtop co-registered ultrasound (US) and AR-PAM systems were constructed and tested in ex vivo human colorectal tissue. In the second phase of the study, a co-registered endorectal AR-PAM imaging system was constructed, and a pilot patient study was conducted on patients with rectal cancer treated with radiation and chemotherapy. To automate the data analysis, we designed and trained convolutional neural networks (PAM-CNN and US-CNN) using mixed ex vivo and in vivo patient data. 22 patients’ ex vivo specimens and five patients’ in vivo images (a total of 2693 US ROIs and 2208 PA ROIs) were used for CNN training and validation. Data from five additional patients were used for testing. A total of 32 participants (mean age, 60 years, range, 35-89 years) were evaluated. Unique PAM imaging markers of complete tumor response were found, specifically recovery of normal submucosal vascular architecture within the treated tumor bed. The PAM-CNN model captured this recovery process and correctly differentiated these changes from a residual tumor tissue. The imaging system remained highly capable of differentiating tumor from normal tissue, achieving an area under receiver operating characteristic curve (AUC) of 0.98 from the five patients tested. By comparison, US-CNN had an AUC of 0.71. As an alternative to CNN, a generalized linear model (GLM) was investigated for classification and results showed that CNN outperformed GLM in classification of both US and PAM images. Ovarian cancer is the leading cause of death among gynecological cancers but is poorly amenable to preoperative diagnosis. In the second project of this thesis, we have investigated the feasibility of “optical biopsy,” using OR-PAM to quantify the microvasculature of ovarian tissue and fallopian tube tissue. The technique was demonstrated using excised human ovary and fallopian tube specimens imaged immediately after surgery. Initially, a commercial software Amira was used to characterize tissue vasculature patterns, and later, an effective and easy-access algorithm was developed to quantify the mean diameter, total length, total volume, and fulfillment rate of tissue vasculature. Our initial results demonstrate the potential of OR-PAM as an imaging tool for quick assessment of ovarian tissue and fallopian tube tissue