X-ray luminescence computed tomography using a focused X-ray beam

Due to the low X-ray photon utilization efficiency and low measurement sensitivity of the electron multiplying charge coupled device (EMCCD) camera setup, the collimator based narrow beam X-ray luminescence computed tomography (XLCT) usually requires a long measurement time. In this paper, we, for the first time, report a focused X-ray beam based XLCT imaging system with measurements by a single optical fiber bundle and a photomultiplier tube (PMT). An X-ray tube with a polycapillary lens was used to generate a focused X-ray beam whose X-ray photon density is 1200 times larger than a collimated X-ray beam. An optical fiber bundle was employed to collect and deliver the emitted photons on the phantom surface to the PMT. The total measurement time was reduced to 12.5 minutes. For numerical simulations of both single and six fiber bundle cases, we were able to reconstruct six targets successfully. For the phantom experiment, two targets with an edge-to-edge distance of 0.4 mm and a center-to-center distance of 0.8 mm were successfully reconstructed by the measurement setup with a single fiber bundle and a PMT.Comment: 39 Pages, 12 Figures, 2 Tables, In submission (under review) to JB

A Small Animal Optical Tomographic Imaging System with Omni-Directional, Non-Contact, Angular-Resolved Fluorescence Measurement Capabilities

The overall goal of this thesis is to develop a new non-contact, whole-body, fluorescence molecular tomography system for small animal imaging. Over the past decade, small animal in vivo imaging has led to a better understanding of many human diseases and improved our ability to develop and test new drugs and medical compounds. Among various imaging modalities, optical imaging techniques have emerged as important tools. In particular, fluorescence and bioluminescence imaging systems have opened new ways for visualizing many molecular pathways inside living animals including gene expression and protein functions. While substantial progress has been made in available prototype and commercial optical imaging systems, there still exist areas for further improvement in the outcome of existing instrumentations. Currently, most small animal optical imaging systems rely on 2D planar imaging that provides limited ability to accurately locate lesions deep inside an animal. Furthermore, most existing tomographic imaging systems use a diffusion model of light propagation, which is of limited accuracy. While more accurate models using the equation of radiative transfer have become available, they have not been widely applied to small animal imaging yet. To overcome the limitations of existing optical small animal imaging systems, a novel imaging system that makes use of the latest hardware and software advances in the field was developed. At the heart of the system is a new double-conical-mirror-based imaging head that enables a single fixed position camera to capture multi-directional views simultaneously. Therefore, the imaging head provides 360-degree measurement data from an entire animal surface in one step. Another benefit provided by this design is the substantial reduction of multiple back-reflections between the animal and mirror surfaces. These back reflections are common in existing mirror-based imaging heads and tend to degrade the quality of raw measurement data. Furthermore, the conical-mirror design offers the capability to measure angular-resolved data from the animal surface. To make full use of this capability, a novel equation of radiative transfer-based ray-transfer operator was introduced to map the spatial and angular information of emitted light on the animal surface to the captured image data. As a result, more data points are involved into the image reconstructions, which leads to a higher image resolution. The performance of the imaging system was evaluated through numerical simulations, experiments using a well-defined tissue phantom, and live-animal studies. Finally, the double reflection mirror scheme presented in this dissertation can be cost-effectively employed with all camera-based imaging systems. The shapes and sizes of mirrors can be varied to accommodate imaging of other objects such as larger animals or human body parts, such as the breast, head, or feet

Fast Radiative-Transfer-Equation-Based Image Reconstruction Algorithms for Non-Contact Diffuse Optical Tomography Systems

It is well known that the radiative transfer equation (RTE) is the most accurate deterministic light propagation model employed in diffuse optical tomography (DOT). RTE-based algorithms provide more accurate tomographic results than codes that rely on the diffusion equation (DE), which is an approximation to the RTE, in scattering dominant media. However, RTE based DOT (RTE-DOT) has limited utility in practice due to its high computational cost and lack of support for general non-contact imaging systems. In this dissertation, I developed fast reconstruction algorithms for RTE-based DOT (RTE-DOT), which consists of three independent components: an efficient linear solver for forward problems, an improved optimization solver for inverse problem, and the first light propagation model in free space that fully considers the angular dependency, which can provide a suitable measurement operator for RTE-DOT. This algorithm is validated and evaluated with numerical experiments and clinical data. According to these studies, the novel reconstruction algorithm is up to 30 times faster than traditional reconstruction techniques, while achieving comparable reconstruction accuracy

Polarization Sensitive Imaging Techniques Using Quantum Entangled Qubits

The aim of this research is to study imaging techniques using quantum entangled qubits. These techniques extract information about the quantum state of two entangled qubits and corelate the degree of entanglement to each pixel. Imaging information of the underlying structure or material is decoded using the reconstruction of the quantum density matrix along with the calculated entanglement and concurrence levels between the two qubits. Reconstruction of a quantum state and quantum state tomography are of increasing importance in quantum information science. Quantum state tomography is used to describe entanglement of trapped ions [1] and photons [2]. Number of experiments were demonstrated in quantum computing, quantum communication and quantum networks where the quantum state density matrix was reconstructed from a set of experimental measurements [2-11]. It is also clear that quantum sensing, quantum computing and quantum imaging techniques can outperform current classical systems in certain areas [12-15]. Yet very little work was done to experimentally apply quantum imaging techniques to study and image birefringent materials. In 1935, Einstein, Podolsky and Rosen published the famous EPR paradox [16], underlining the incomplete description of physical reality and the requirement of hidden variables. The phenomenon involved quantum entanglement and it opened opportunities for research in numerous fields of study. In optical communication entangled states were applied to quantum information theory, quantum teleportation and quantum cryptography [16-29]. Probably the most popular applications are in quantum computing. The superposition of entangled states represents quantum bits in combination of both logical one and zero simultaneously. For the last few decades, very few experiments were conducted to utilize quantum entanglement in imaging or material characterization applications. The proposed study develops and describes quantum imaging and characterization techniques using the increased sensitivity and quantum-entanglement of the bosonic states. Quantum mechanics accommodates co-existence of two completely indistinguishable photon particles separated in space. One of the entangled photons can be made to interact with the investigated sample. The sample is placed on a microscope slide and scanned in the transverse and/or axial plane. The localized birefringence changes the polarization of the photon, and these changes translate into a reduction of the coincidence rate of the entangled photons. This research also presents the first experimental imaging implementation of polarization sensitive quantum optical coherence tomography (PS-QOCT), a technique introduced years ago by a group at Boston University. The idea is simple enough: it consists of a fourth-order interferometric technique that uses quantum-entangled photons, generated in a type-II crystal via spontaneous parametric down-conversion. In contrast with its classical counterpart, PS-QOCT provides resolution enhancement and immunity to even- order group velocity dispersion. A proof-of-principle of this technique was demonstrated a while ago [30] using a type-II collinear phase-matching in a BBO crystal pumped by a Ti:Shapphire picosecond pulsed laser source. However, imaging measurements have not been reported in [30]. The work in this thesis provides the missing data. The goal of this research work was to develop and study quantum imaging techniques. Apply entangled qubits to characterize birefringence and reconstruct images from entanglement and concurrence levels. Quantum imaging technique was also used to examine healthy and cancerous human lung tissues. Well- defined concurrence and entanglement images of birefringence were obtained in lung tissue with melanoma while no birefringence was detected in healthy samples. Melanoma is an aggressive tumor and has a propensity to metastasize to lymph nodes in lungs, liver and virtually any other site of the body. Our work suggests that quantum imaging could eventually assist with the medical diagnosis of metastatic melanoma in the future

Fluorescence molecular tomography: Principles and potential for pharmaceutical research

Fluorescence microscopic imaging is widely used in biomedical research to study molecular and cellular processes in cell culture or tissue samples. This is motivated by the high inherent sensitivity of fluorescence techniques, the spatial resolution that compares favorably with cellular dimensions, the stability of the fluorescent labels used and the sophisticated labeling strategies that have been developed for selectively labeling target molecules. More recently, two and three-dimensional optical imaging methods have also been applied to monitor biological processes in intact biological organisms such as animals or even humans. These whole body optical imaging approaches have to cope with the fact that biological tissue is a highly scattering and absorbing medium. As a consequence, light propagation in tissue is well described by a diffusion approximation and accurate reconstruction of spatial information is demanding. While in vivo optical imaging is a highly sensitive method, the signal is strongly surface weighted, i.e., the signal detected from the same light source will become weaker the deeper it is embedded in tissue, and strongly depends on the optical properties of the surrounding tissue. Derivation of quantitative information, therefore, requires tomographic techniques such as fluorescence molecular tomography (FMT), which maps the three-dimensional distribution of a fluorescent probe or protein concentration. The combination of FMT with a structural imaging method such as X-ray computed tomography (CT) or Magnetic Resonance Imaging (MRI) will allow mapping molecular information on a high definition anatomical reference and enable the use of prior information on tissue’s optical properties to enhance both resolution and sensitivity. Today many of the fluorescent assays originally developed for studies in cellular systems have been successfully translated for experimental studies in animals. The opportunity of monitoring molecular processes non-invasively in the intact organism is highly attractive from a diagnostic point of view but even more so for the drug developer, who can use the techniques for proof-of-mechanism and proof-of-efficacy studies. This review shall elucidate the current status and potential of fluorescence tomography including recent advances in multimodality imaging approaches for preclinical and clinical drug development

Multi-modal molecular diffuse optical tomography system for small animal imaging

A multi-modal optical imaging system for quantitative 3D bioluminescence and functional diffuse imaging is presented, which has no moving parts and uses mirrors to provide multi-view tomographic data for image reconstruction. It is demonstrated that through the use of trans-illuminated spectral near infrared measurements and spectrally constrained tomographic reconstruction, recovered concentrations of absorbing agents can be used as prior knowledge for bioluminescence imaging within the visible spectrum. Additionally, the first use of a recently developed multi-view optical surface capture technique is shown and its application to model-based image reconstruction and free-space light modelling is demonstrated. The benefits of model-based tomographic image recovery as compared to 2D planar imaging are highlighted in a number of scenarios where the internal luminescence source is not visible or is confounding in 2D images. The results presented show that the luminescence tomographic imaging method produces 3D reconstructions of individual light sources within a mouse-sized solid phantom that are accurately localised to within 1.5mm for a range of target locations and depths indicating sensitivity and accurate imaging throughout the phantom volume. Additionally the total reconstructed luminescence source intensity is consistent to within 15% which is a dramatic improvement upon standard bioluminescence imaging. Finally, results from a heterogeneous phantom with an absorbing anomaly are presented demonstrating the use and benefits of a multi-view, spectrally constrained coupled imaging system that provides accurate 3D luminescence images

Optical projection tomography for whole organ imaging

In the past twenty years, far-reaching studies of molecular and cellular processes have reached a milestone in their maturation, and the knowledge from these studies was ready to apply at higher organizational levels. At that time, rodent models were long established. However, methods were inappropriate to image a whole rodent organ, such as the mouse brain, which drove the emergence of a new range of imaging techniques, later gathered under the name mesoscopy. Mesoscopic techniques filled a gap between classical microscopy and medical imaging techniques, such as magnetic resonance imaging, and X-ray computed tomography. They allow the acquisition of centimeter-sized samples. In this thesis, we focus on one of these mesoscopic imaging techniques called optical projection tomography, or OPT, and its potential application to Alzheimer's disease (AD) research. We review the fundamentals of OPT and describe the filtered back-projection algorithm, which is the primary tomographic reconstruction method of this technique. We also go through the implementation of OPT for whole mouse brain imaging, including sample preparation. We show that OPT is suitable to image the whole brain anatomy based on endogenous fluorescence, and the whole neural vasculature as well as amyloid plaques (a hallmark of AD) with adequate fluorescent markers. Then, we dwell on the characterization of OPT instruments. We give some insights on the instrument point spread function and discuss the influence of the number of projections on the quality of the reconstructed image. Afterward, we illustrate the application of OPT to study amyloidosis progression in a preliminary cross-sectional study, where we have used supervised learning to quantify the amyloid plaque load. In this study, we show that OPT can be used to quantify amyloidosis in whole mouse brains and that comparison between individuals of different age can be performed. Imaging of a whole mouse brain is unquestionably necessary. At this scale though, it has some constraints. We present the limitations of OPT, and we share how we think they can be circumvented by combining this modality with another microscopy technique, namely structured illumination microscopy. We see that this other microscopy technique has the potential to produce high-resolution zooms in selected regions of interest based on a prior OPT acquisition. The results presented in this work have led to the duplication of our OPT instrument in Lund University, and we hope they will help to foster advances in OPT and broaden its range of application. We also hope that this work will contribute to making OPT more accessible and user-friendly

A dark field illumination probe linked to Raman spectroscopy for non-invasivety determination of ocular biomarkers

For early and effective diagnosis of eye diseases, acquiring biochemical information in the eye is preferred. However, it is obtained by performing a biopsy of the eye tissue. This poses a risk to the integrity of the eye and cannot be performed on a regular basis. Raman spectrometry is a potential and powerful tool for the non-invasive investigation of biochemical information. The challenge to use it in an ophthalmic application is the essential of a high-power laser direct shining through the eye, which raises safety concerns for potential retinal damage .In this thesis, biomedical applications of Raman spectroscopy are explored for eye disease biomarkers and ocular drug measurements in ex vitro, in vitro and in vivo. To ensure a safety measurement by projecting a laser in the eye, two types of dark-field illumination probes are designed, manufactured and validated in conjunction with confocal Raman spectroscopy (CRS) to avoid light damage of the retina. Furthermore, a non-contact dark-field illumination method for the same purpose is proposed and theoretically validated