Systems and Methods for the Spectral Calibration of Swept Source Optical Coherence Tomography Systems

This dissertation relates to the transition of the state of the art of swept source optical coherence tomography (SS-OCT) systems to a new realm in which the image acquisition speed is improved by an order of magnitude. With the aid of a better quality imaging technology, the speed-up factor will considerably shorten the eye-exam clinical visits which in turn improves the patient and doctor interaction experience. These improvements will directly lower associated medical costs for eye-clinics and patients worldwide. There are several other embodiments closely related to Optical Coherence Tomography (OCT) that could benefit from the ideas presented in this dissertation including: optical coherence microscopy (OCM), full-field OCT (FF-OCT), optical coherence elastography (OCE), optical coherence tomography angiography (OCT-A), anatomical OCT (aOCT), optical coherence photoacoustic microscopy (OC-PAM), micro optical coherence tomography (µ OCT), among others. In recent decades, OCT has established itself as the de-facto imaging process that most ophthalmologists refer to in their clinical practices. In a broader sense, optical coherence tomography is used in applications when low penetration and high resolution are desired. These applications include different fields of biomedical sciences including cardiology, dermatology, and pulmonary related sciences. Many other industrial applications including quality control and precise measurements have also been reported that are related to the OCT technology. Every new iteration of OCT technology has always come about with advanced signal processing and data acquisition algorithms using mixed-signal architectures, calibration and signal processing techniques. The existing industrial practices towards data acquisition, processing, and image creation relies on conventional signal processing design flows, which extensively employ continuous/discrete techniques that are both time-consuming and costly. The ideas presented in this dissertation can take the technology to a new dimension of quality of service

Optical Coherence Tomography Distal Sensor Based Handheld Microsurgical Tools

Microsurgery is typically differentiated from a general surgery in that it requires a precise sub-millimeter manipulation that could only be achievable under optical magnification. For instance, microsurgeons use surgical microscopes to view surgical sites and train themselves several years to acquire surgical skills to perform the delicate procedures. However, such microsurgical approach imposes considerable physical stress and mental fatigue on the surgeons and these could be sources for surgical risks and complications. For these reasons, a variety of robotic based surgical guidance methods have been developed and studied with the hope of providing safer and more precise microsurgery. These robotic arm based systems have been developed to provide precise tool movement and to remove physiological hand tremor, which is one of the main limiting factors that prevents precise tool manipulation. In another approaches use simpler system that adds robotic functions to existing handheld surgical tools. It is a hybrid system that incorporates the advantages of conventional manual system and robot-assist system. The advantages of such hybrid handheld systems include portability, disposability, and elimination of the large robotic-assist systems in complex surgical environment. The most critical benefit of the hybrid handheld system is its ease of use since it allows surgeons to manipulate tools mostly using their hand. However due to the imprecise nature of tool control using hands, tool tracking is more critical in handheld microsurgical tool systems than that of robotic arm systems. In general, the accuracy of the tool control is largely determined by the resolution of the sensors and the actuators. Therefore, it is essential to develop a real-time high resolution sensor in order to develop a practical microsurgical tools. For this reason, a novel intuitive targeting and tracking scheme that utilizes a common-path swept source optical coherence tomography (CP-SSOCT) distal sensor was developed integrated with handheld microsurgical tools. To achieve micron-order precision control, a reliable and accurate OCT distal sensing method was developed. The method uses a prediction algorithm is necessary to compensate for the system delay associated with the computational, mechanical and electronic latencies. Due to the multi-layered structure of retina, it was also necessary to develop effective surface detection methods rather than simple peak detection. The OCT distal sensor was integrated into handheld motion-guided micro-forceps system for highly accurate depth controlled epiretinal membranectomy. A touch sensor and two motors were used in the forceps design to minimize the motion artifact induced by squeezing, and to independently control the depth guidance of the tool-tip and the grasping action. We also built a depth guided micro-injector system that enables micro-injection with precise injection depth control. For these applications, a smart motion monitoring and a guiding algorithm were developed to provide precise and intuitive freehand control. Finally, phantom and ex-vivo bovine eye experiments were performed to evaluate the performance of the proposed OCT distal sensor and validate the effectiveness of the depth-guided micro-forceps and micro-injector over the freehand performance

Advanced photonic and electronic systems - WILGA 2017

WILGA annual symposium on advanced photonic and electronic systems has been organized by young scientist for young scientists since two decades. It traditionally gathers more than 350 young researchers and their tutors. Ph.D students and graduates present their recent achievements during well attended oral sessions. Wilga is a very good digest of Ph.D. works carried out at technical universities in electronics and photonics, as well as information sciences throughout Poland and some neighboring countries. Publishing patronage over Wilga keep Elektronika technical journal by SEP, IJET by PAN and Proceedings of SPIE. The latter world editorial series publishes annually more than 200 papers from Wilga. Wilga 2017 was the XL edition of this meeting. The following topical tracks were distinguished: photonics, electronics, information technologies and system research. The article is a digest of some chosen works presented during Wilga 2017 symposium. WILGA 2017 works were published in Proc. SPIE vol.10445

Development of temporal phase unwrapping algorithms for depth-resolved measurements using an electronically tuned Ti:Sa laser

This thesis is concerned with (a) the development of full-field, multi-axis and phase contrast wavelength scanning interferometer, using an electronically tuned CW Ti:Sa laser for the study of depth resolved measurements in composite materials such as GFRPs and (b) the development of temporal phase unwrapping algorithms for depth re-solved measurements. Item (a) was part of the ultimate goal of successfully extracting the 3-D, depth-resolved, constituent parameters (Young s modulus E, Poisson s ratio v etc.) that define the mechanical behaviour of composite materials like GFRPs. Considering the success of OCT as an imaging modality, a wavelength scanning interferometer (WSI) capable of imaging the intensity AND the phase of the interference signal was proposed as the preferred technique to provide the volumetric displacement/strain fields (Note that displacement/strain fields are analogous to phase fields and thus a phase-contrast interferometer is of particular interest in this case). These would then be passed to the VFM and yield the sought parameters provided the loading scheme is known. As a result, a number of key opto-mechanical hardware was developed. First, a multiple channel (x6) tomographic interferometer realised in a Mach-Zehnder arrangement was built. Each of the three channels would provide the necessary information to extract the three orthogonal displacement/strain components while the other three are complementary and were included in the design in order to maximize the penetration depth (sample illuminated from both sides). Second, a miniature uniaxial (tensile and/or compression) loading machine was designed and built for the introduction of controlled and low magnitude displacements. Last, a rotation stage for the experimental determination of the sensitivity vectors and the re-registration of the volumetric data from the six channels was also designed and built. Unfortunately, due to the critical failure of the Ti:Sa laser data collection using the last two items was not possible. However, preliminary results at a single wavelength suggested that the above items work as expected. Item (b) involved the development of an optical sensor for the dynamic monitoring of wavenumber changes during a full 100 nm scan. The sensor is comprised of a set of four wedges in a Fizeau interferometer setup that became part of the multi-axis interferometer (7th channel). Its development became relevant due to the large amount of mode-hops present during a full scan of the Ti:Sa source. These are associated to the physics of the laser and have the undesirable effect of randomising the signal and thus preventing successful depth reconstructions. The multi-wedge sensor was designed so that it provides simultaneously high wavenumber change resolution and immunity to the large wavenumber jumps from the Ti:Sa. The analysis algorithms for the extraction of the sought wavenumber changes were based on 2-D Fourier transform method followed by temporal phase unwrapping. At first, the performance of the sensor was tested against that of a high-end commercial wavemeter for a limited scan of 1nm. A root mean square (rms) difference in measured wavenumber shift between the two of ∼4 m-1 has been achieved, equivalent to an rms wavelength shift error of ∼0.4 pm. Second, by resampling the interference signal and the wavenumber-change axis onto a uniformly sampled k-space, depth resolutions that are close to the theoretical limits were achieved for scans of up to 37 nm. Access of the full 100 nm range that is characterised by wavelength steps down to picometers level was achieved by introducing a number of improvements to the original temporal phase unwrapping algorithm reported in ref [1] tailored to depth resolved measurements. These involved the estimation and suppression of intensity background artefacts, improvements on the 2-D Fourier transform phase detection based on a previously developed algorithm in ref [2] and finally the introduction of two modifications to the original TPU. Both approaches are adaptive and involve signal re-referencing at regular intervals throughout the scan. Their purpose is to compensate for systematic and non-systematic errors owing to a small error in the value of R (a scaling factor applied to the lower sensitivity wedge phase-change signal used to unwrap the higher sensitivity one), or small changes in R with wavelength due to the possibility of a mismatch in the refractive dispersion curves of the wedges and/or a mismatch in the wedge angles. A hybrid approach combining both methods was proposed and used to analyse the data from each of the four wedges. It was found to give the most robust results of all the techniques considered, with a clear Fourier peak at the expected frequency, with significantly reduced spectral artefacts and identical depth resolutions for all four wedges of 2.2 μm measured at FWHM. The ability of the phase unwrapping strategy in resolving the aforementioned issues was demonstrated by successfully measuring the absolute thickness of four fused silica glasses using real experimental data. The results were compared with independent micrometer measurements and showed excellent agreement. Finally, due to the lack of additional experimental data and in an attempt to justify the validity of the proposed temporal phase unwrapping strategy termed as the hybrid approach, a set of simulations that closely matched the parameters characterising the real experimental data set analysed were produced and were subsequently analysed. The results of this final test justify that the various fixes included in the hybrid approach have not evolved to solve the problems of a particular data set but are rather of general nature thereby, highlighting its importance for PC-WSI applications concerning the processing and analysis of large scans

Optical coherence tomography methods using 2-D detector arrays

Optical coherence tomography (OCT) is a non-invasive, non-contact optical technique that allows cross-section imaging of biological tissues with high spatial resolution, high sensitivity and high dynamic range. Standard OCT uses a focused beam to illuminate a point on the target and detects the signal using a single photodetector. To acquire transverse information, transversal scanning of the illumination point is required. Alternatively, multiple OCT channels can be operated in parallel simultaneously; parallel OCT signals are recorded by a two-dimensional (2D) detector array. This approach is known as Parallel-detection OCT. In this thesis, methods, experiments and results using three parallel OCT techniques, including full -field (time-domain) OCT (FF-OCT), full-field swept-source OCT (FF-SS-OCT) and line-field Fourier-domain OCT (LF-FD-OCT), are presented. Several 2D digital cameras of different formats have been used and evaluated in the experiments of different methods. With the LF-FD-OCT method, photography equipment, such as flashtubes and commercial DSLR cameras have been equipped and tested for OCT imaging. The techniques used in FF-OCT and FF-SS-OCT are employed in a novel wavefront sensing technique, which combines OCT methods with a Shack-Hartmann wavefront sensor (SH-WFS). This combination technique is demonstrated capable of measuring depth-resolved wavefront aberrations, which has the potential to extend the applications of SH-WFS in wavefront-guided biomedical imaging techniques

MEMS Technology for Biomedical Imaging Applications

Biomedical imaging is the key technique and process to create informative images of the human body or other organic structures for clinical purposes or medical science. Micro-electro-mechanical systems (MEMS) technology has demonstrated enormous potential in biomedical imaging applications due to its outstanding advantages of, for instance, miniaturization, high speed, higher resolution, and convenience of batch fabrication. There are many advancements and breakthroughs developing in the academic community, and there are a few challenges raised accordingly upon the designs, structures, fabrication, integration, and applications of MEMS for all kinds of biomedical imaging. This Special Issue aims to collate and showcase research papers, short commutations, perspectives, and insightful review articles from esteemed colleagues that demonstrate: (1) original works on the topic of MEMS components or devices based on various kinds of mechanisms for biomedical imaging; and (2) new developments and potentials of applying MEMS technology of any kind in biomedical imaging. The objective of this special session is to provide insightful information regarding the technological advancements for the researchers in the community

Multidimensional Data Processing for Optical Coherence Tomography Imaging

Optical Coherence Tomography (OCT) is a medical imaging technique which distinguishes itself by acquiring microscopic resolution images in-vivo at millimeter scale fields of view. The resulting in images are not only high-resolution, but often multi-dimensional to capture 3-D biological structures or temporal processes. The nature of multi-dimensional data presents a unique set of challenges to the OCT user that include acquiring, storing, and handling very large datasets, visualizing and understanding the data, and processing and analyzing the data. In this dissertation, three of these challenges are explored in depth: sub-resolution temporal analysis, 3-D modeling of fiber structures, and compressed sensing of large, multi-dimensional datasets. Exploration of these problems is followed by proposed solutions and demonstrations which rely on tools from multiple research areas including digital image filtering, image de-noising, and sparse representation theory. Combining approaches from these fields, advanced solutions were developed to produce new and groundbreaking results. High-resolution video data showing cilia motion in unprecedented detail and scale was produced. An image processing method was used to create the first 3-D fiber model of uterine tissue from OCT images. Finally, a compressed sensing approach was developed which we show to guarantee high accuracy image recovery of more complicated, clinically relevant, samples than had been previously demonstrated. The culmination of these methods represents a step forward in OCT image analysis, showing that these cutting edge tools can also be applied to OCT data and in the future be employed in a clinical setting

Development and Characterization of a Dispersion-Encoded Method for Low-Coherence Interferometry

This Open Access book discusses an extension to low-coherence interferometry by dispersion-encoding. The approach is theoretically designed and implemented for applications such as surface profilometry, polymeric cross-linking estimation and the determination of thin-film layer thicknesses. During a characterization, it was shown that an axial measurement range of 79.91 µm with an axial resolution of 0.1 nm is achievable. Simultaneously, profiles of up to 1.5 mm in length were obtained in a scan-free manner. This marked a significant improvement in relation to the state-of-the-art in terms of dynamic range. Also, the axial and lateral measurement range were decoupled partially while functional parameters such as surface roughness were estimated. The characterization of the degree of polymeric cross-linking was performed as a function of the refractive index. It was acquired in a spatially-resolved manner with a resolution of 3.36 x 10-5. This was achieved by the development of a novel mathematical analysis approach

Combinatorial optimisation for arterial image segmentation.

Cardiovascular disease is one of the leading causes of the mortality in the western world. Many imaging modalities have been used to diagnose cardiovascular diseases. However, each has different forms of noise and artifacts that make the medical image analysis field important and challenging. This thesis is concerned with developing fully automatic segmentation methods for cross-sectional coronary arterial imaging in particular, intra-vascular ultrasound and optical coherence tomography, by incorporating prior and tracking information without any user intervention, to effectively overcome various image artifacts and occlusions. Combinatorial optimisation methods are proposed to solve the segmentation problem in polynomial time. A node-weighted directed graph is constructed so that the vessel border delineation is considered as computing a minimum closed set. A set of complementary edge and texture features is extracted. Single and double interface segmentation methods are introduced. Novel optimisation of the boundary energy function is proposed based on a supervised classification method. Shape prior model is incorporated into the segmentation framework based on global and local information through the energy function design and graph construction. A combination of cross-sectional segmentation and longitudinal tracking is proposed using the Kalman filter and the hidden Markov model. The border is parameterised using the radial basis functions. The Kalman filter is used to adapt the inter-frame constraints between every two consecutive frames to obtain coherent temporal segmentation. An HMM-based border tracking method is also proposed in which the emission probability is derived from both the classification-based cost function and the shape prior model. The optimal sequence of the hidden states is computed using the Viterbi algorithm. Both qualitative and quantitative results on thousands of images show superior performance of the proposed methods compared to a number of state-of-the-art segmentation methods