306 research outputs found

    Computational Imaging for Phase Retrieval and Biomedical Applications

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    In conventional imaging, optimizing hardware is prioritized to enhance image quality directly. Digital signal processing is viewed as supplementary. Computational imaging intentionally distorts images through modulation schemes in illumination or sensing. Then its reconstruction algorithms extract desired object information from raw data afterwards. Co-designing hardware and algorithms reduces demands on hardware and achieves the same or even better image quality. Algorithm design is at the heart of computational imaging, with model-based inverse problem or data-driven deep learning methods as approaches. This thesis presents research work from both perspectives, with a primary focus on the phase retrieval issue in computational microscopy and the application of deep learning techniques to address biomedical imaging challenges. The first half of the thesis begins with Fourier ptychography, which was employed to overcome chromatic aberration problems in multispectral imaging. Then, we proposed a novel computational coherent imaging modality based on Kramers-Kronig relations, aiming to replace Fourier ptychography as a non-iterative method. While this approach showed promise, it lacks certain essential characteristics of the original Fourier ptychography. To address this limitation, we introduced two additional algorithms to form a whole package scheme. Through comprehensive evaluation, we demonstrated that the combined scheme outperforms Fourier ptychography in achieving high-resolution, large field-of-view, aberration-free coherent imaging. The second half of the thesis shifts focus to deep-learning-based methods. In one project, we optimized the scanning strategy and image processing pipeline of an epifluorescence microscope to address focus issues. Additionally, we leveraged deep-learning-based object detection models to automate cell analysis tasks. In another project, we predicted the polarity status of mouse embryos from bright field images using adapted deep learning models. These findings highlight the capability of computational imaging to automate labor-intensive processes, and even outperform humans in challenging tasks.</p

    Development of polarization-resolved optical scanning microscopy imaging techniques to study biomolecular organizations

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    Light, as electromagnetic radiation, conveys energy through space and time via fluctuations in electric and magnetic fields. This thesis explores the interaction of light and biological structures through polarization-resolved imaging techniques. Light microscopy, and polarization analysis enable the examination of biological entities. Biological function often centers on chromatin, the genetic material composed of DNA wrapped around histone proteins within cell nuclei. This structure's chiral nature gives rise to interactions with polarized light. This research encompasses three main aspects. Firstly, an existing multimodal Circular Intensity Differential Scattering (CIDS) and fluorescence microscopy are upgraded into an open configuration to be integrated with other modalities. Secondly, a novel cell classification method employing CIDS and a phasor representation is introduced. Thirdly, polarization analysis of fluorescence emission is employed for pathological investigations. Accordingly, the thesis is organized into three chapters. Chapter 1 lays the theoretical foundation for light propagation and polarization, outlining the Jones and Stokes-Mueller formalisms. The interaction between light and optical elements, transmission, and reflection processes are discussed. Polarized light's ability to reveal image contrast in polarizing microscopes, linear and nonlinear polarization-resolved microscopy, and Mueller matrix microscopy as a comprehensive technique for studying biological structures are detailed. Chapter 2 focuses on CIDS, a label-free light scattering method, including a single point angular spectroscopy mode and scanning microscopy imaging. A significant upgrade of the setup is achieved, incorporating automation, calibration, and statistical analysis routines. An intuitive phasor approach is proposed, enabling image segmentation, cell discrimination, and enhanced interpretation of polarimetric contrast. As a result, image processing programs have been developed to provide automated measurements using polarization-resolved laser scanning microscopy imaging integrated with confocal fluorescence microscopy of cells and chromatin inside cell nuclei, including the use of new types of samples such as progeria cells. Chapter 3 applies a polarization-resolved two-photon excitation fluorescence (2PEF) microscopy to study multicellular cancerous cells. A homemade 2PEF microscope is developed for colon cancer cell analysis. The integration of polarization and fluorescence techniques leads to a comprehensive understanding of the molecular orientation within samples, particularly useful for cancer diagnosis. Overall, this thesis presents an exploration of polarization-resolved imaging techniques for studying biological structures, encompassing theory, experimental enhancements, innovative methodologies, and practical applications

    Roadmap for optical tweezers

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    Artículo escrito por un elevado número de autores, solo se referencian el que aparece en primer lugar, el nombre del grupo de colaboración, si le hubiere, y los autores pertenecientes a la UAMOptical tweezers are tools made of light that enable contactless pushing, trapping, and manipulation of objects, ranging from atoms to space light sails. Since the pioneering work by Arthur Ashkin in the 1970s, optical tweezers have evolved into sophisticated instruments and have been employed in a broad range of applications in the life sciences, physics, and engineering. These include accurate force and torque measurement at the femtonewton level, microrheology of complex fluids, single micro- and nano-particle spectroscopy, single-cell analysis, and statistical-physics experiments. This roadmap provides insights into current investigations involving optical forces and optical tweezers from their theoretical foundations to designs and setups. It also offers perspectives for applications to a wide range of research fields, from biophysics to space explorationEuropean Commission (Horizon 2020, Project No. 812780

    Engineering a Low-Cost Remote Sensing Capability for Deep-Space Applications

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    Systems engineering (SE) has been a useful tool for providing objective processes to breaking down complex technical problems to simpler tasks, while concurrently generating metrics to provide assurance that the solution is fit-for-purpose. Tailored forms of SE have also been used by cubesat mission designers to assist in reducing risk by providing iterative feedback and key artifacts to provide managers with the evidence to adjust resources and tasking for success. Cubesat-sized spacecraft are being planned, built and in some cases, flown to provide a lower-cost entry point for deep-space exploration. This is particularly important for agencies and countries with lower space exploration budgets, where specific mission objectives can be used to develop tailored payloads within tighter constraints, while also returning useful scientific results or engineering data. In this work, a tailored SE tradespace approach was used to help determine how a 6 unit (6U) cubesat could be built from commercial-off-the-shelf (COTS)-based components and undertake remote sensing missions near Mars or near-Earth Asteroids. The primary purpose of these missions is to carry a hyperspectral sensor sensitive to 600-800nm wavelengths (hereafter defined as “red-edge”), that will investigate mineralogy characteristics commonly associated with oxidizing and hydrating environments in red-edge. Minerals of this type remain of high interest for indicators of present or past habitability for life, or active geologic processes. Implications of operating in a deep-space environment were considered as part of engineering constraints of the design, including potential reduction of available solar energy, changes in thermal environment and background radiation, and vastly increased communications distances. The engineering tradespace analysis identified realistic COTS options that could satisfy mission objectives for the 6U cubesat bus while also accommodating a reasonable degree of risk. The exception was the communication subsystem, in which case suitable capability was restricted to one particular option. This analysis was used to support an additional trade investigation into the type of sensors that would be most suitable for building the red-edge hyperspectral payload. This was in part constrained by ensuring not only that readily available COTS sensors were used, but that affordability, particularly during a geopolitical environment that was affecting component supply surety and access to manufacturing facilities, was optimized. It was found that a number of sensor options were available for designing a useful instrument, although the rapid development and life-of-type issues with COTS sensors restricted the ability to obtain useful metrics on their performance in the space environment. Additional engineering testing was conducted by constructing hyperspectral sensors using sensors popular in science, technology, engineering and mathematics (STEM) contexts. Engineering and performance metrics of the payload containing the sensors was conducted; and performance of these sensors in relevant analogous environments. A selection of materials exhibiting spectral phenomenology in the red-edge portion of the spectrum was used to produce metrics on the performance of the sensors. It was found that low-cost cameras were able to distinguish between most minerals, although they required a wider spectral range to do so. Additionally, while Raspberry Pi cameras have been popular with scientific applications, a low-cost camera without a Bayer filter markedly improved spectral sensitivity. Consideration for space-environment testing was also trialed in additional experiments using high-altitude balloons to reach the near-space environment. The sensor payloads experienced conditions approximating the surface of Mars, and results were compared with Landsat 7, a heritage Earth sensing satellite, using a popular vegetation index. The selected Raspberry Pi cameras were able to provide useful results from near-space that could be compared with space imagery. Further testing incorporated comparative analysis of custom-built sensors using readily available Raspberry Pi and astronomy cameras, and results from Mastcam and Mastcam/z instruments currently on the surface of Mars. Two sensor designs were trialed in field settings possessing Mars-analogue materials, and a subset of these materials were analysed using a laboratory-grade spectro-radiometer. Results showed the Raspberry Pi multispectral camera would be best suited for broad-scale indications of mineralogy that could be targeted by the pushbroom sensor. This sensor was found to possess a narrower spectral range than the Mastcam and Mastcam/z but was sensitive to a greater number of bands within this range. The pushbroom sensor returned data on spectral phenomenology associated with attributes of Minerals of the type found on Mars. The actual performance of the payload in appropriate conditions was important to provide critical information used to risk reduce future designs. Additionally, the successful outcomes of the trials reduced risk for their application in a deep space environment. The SE and practical performance testing conducted in this thesis could be developed further to design, build and fly a hyperspectral sensor, sensitive to red-edge wavelengths, on a deep-space cubesat mission. Such a mission could be flown at reasonable cost yet return useful scientific and engineering data

    Roadmap for optical tweezers

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    Optical tweezers are tools made of light that enable contactless pushing, trapping, and manipulation of objects, ranging from atoms to space light sails. Since the pioneering work by Arthur Ashkin in the 1970s, optical tweezers have evolved into sophisticated instruments and have been employed in a broad range of applications in the life sciences, physics, and engineering. These include accurate force and torque measurement at the femtonewton level, microrheology of complex fluids, single micro- and nano-particle spectroscopy, single-cell analysis, and statistical-physics experiments. This roadmap provides insights into current investigations involving optical forces and optical tweezers from their theoretical foundations to designs and setups. It also offers perspectives for applications to a wide range of research fields, from biophysics to space exploration.journal articl
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