1,109 research outputs found

    Confocal Microscopy and Three-Dimensional Reconstruction of Thick, Transparent, Vital Tissue

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    The three-dimensional visualization of the 400 micron thick, transparent, in situ cornea is described to demonstrate the use of confocal light microscopy for noninvasive imaging of living cells and thick tissues in their normal, vital conditions. Specimen preparation and physiological stability, as well as light attenuation corrections are critical to data acquisition. The technique to provide mechanical stability of the specimen during the duration of the image acquisition is explained. A laser scanning confocal light microscope (LSCM) was used to obtain optical serial sections from rabbit eyes that were freshly removed and placed in a physiological Ringer\u27s solution. This study demonstrates the capability of the confocal light microscope to obtain a series of high contrast images, with a depth resolution of one micron, across the full thickness of living, transparent tissue. The problems of nonisotropic sampling and the limited eight-bit dynamic range are discussed. The three-dimensional reconstructions were obtained by computer graphics using the volume visualization projection technique. The three-dimensional visualization of the cornea in the in situ eye is presented as an example of image understanding of thick, viable biological cells and tissues. Finally, the criterion of image fidelity is explained. The techniques of confocal light microscopy with its enhanced lateral and axial resolution, improved image contrast, and volume visualization provides microscopists with new techniques for the observation of vital cells and tissues, both in vivo and in vitro

    Visualisation of Articular Cartilage Microstructure

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    This thesis developed image processing techniques enabling the detection and segregation of biological three dimensional images into its component features based upon shape and relative size of the features detected. The work used articular cartilage images and separated fibrous components from the cells and background noise. Measurement of individual components and their recombination into a composite image are possible. Developed software was used to analyse the development of hyaline cartilage in developing sheep embryos

    Quantifying the Surface Geometry of Titanium Implant Material by Different Methods of Analysis

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    Biomaterial implant manufacturers have used rough surfaces to ensure better biocompatibility, less rejection and better adaptation of implants in the body. Proper characterization of biological interactions and biocompatibility of biomaterials requires a thorough understanding of surface complexity. Surface roughness has often been shown to be important in influencing biological reactions with the surface. Previous communications from our laboratory have described a dynamic active vision system (MVS camera) capable of measuring three-dimensional coordinates of titanium implant material surfaces. Fractal analysis, due to its straightforward relationship to texture, is used to characterize the degree of irregularity of a surface and is expressed over a range of scales with the variation method. This paper compares the fractal approach with the results of image analysis, tactile profilometry, and confocal microscopy. The data obtained in these studies show that surface fractal dimension, in particular, can be a valuable parameter to describe the complexity of surface of titanium implant materials

    Applications of Surface Metrology to Issues in Art

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    This work investigates applying surface metrology techniques to issues in art, such as, restoration and identification. It seeks possible areas of collaboration between the Worcester Art Museum and Worcester Polytechnic Institute\u27s Surface Metrology Lab. Surface metrology is the study of measurement and analysis of surface textures, or roughness. We have completed an experiment to demonstrate that scanning laser microscopy and scale-sensitve fractal analysis used on paintings can discriminate brush types and paints

    A Modular and Open-Source Framework for Virtual Reality Visualisation and Interaction in Bioimaging

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    Life science today involves computational analysis of a large amount and variety of data, such as volumetric data acquired by state-of-the-art microscopes, or mesh data from analysis of such data or simulations. The advent of new imaging technologies, such as lightsheet microscopy, has resulted in the users being confronted with an ever-growing amount of data, with even terabytes of imaging data created within a day. With the possibility of gentler and more high-performance imaging, the spatiotemporal complexity of the model systems or processes of interest is increasing as well. Visualisation is often the first step in making sense of this data, and a crucial part of building and debugging analysis pipelines. It is therefore important that visualisations can be quickly prototyped, as well as developed or embedded into full applications. In order to better judge spatiotemporal relationships, immersive hardware, such as Virtual or Augmented Reality (VR/AR) headsets and associated controllers are becoming invaluable tools. In this work we present scenery, a modular and extensible visualisation framework for the Java VM that can handle mesh and large volumetric data, containing multiple views, timepoints, and color channels. scenery is free and open-source software, works on all major platforms, and uses the Vulkan or OpenGL rendering APIs. We introduce scenery's main features, and discuss its use with VR/AR hardware and in distributed rendering. In addition to the visualisation framework, we present a series of case studies, where scenery can provide tangible benefit in developmental and systems biology: With Bionic Tracking, we demonstrate a new technique for tracking cells in 4D volumetric datasets via tracking eye gaze in a virtual reality headset, with the potential to speed up manual tracking tasks by an order of magnitude. We further introduce ideas to move towards virtual reality-based laser ablation and perform a user study in order to gain insight into performance, acceptance and issues when performing ablation tasks with virtual reality hardware in fast developing specimen. To tame the amount of data originating from state-of-the-art volumetric microscopes, we present ideas how to render the highly-efficient Adaptive Particle Representation, and finally, we present sciview, an ImageJ2/Fiji plugin making the features of scenery available to a wider audience.:Abstract Foreword and Acknowledgements Overview and Contributions Part 1 - Introduction 1 Fluorescence Microscopy 2 Introduction to Visual Processing 3 A Short Introduction to Cross Reality 4 Eye Tracking and Gaze-based Interaction Part 2 - VR and AR for System Biology 5 scenery — VR/AR for Systems Biology 6 Rendering 7 Input Handling and Integration of External Hardware 8 Distributed Rendering 9 Miscellaneous Subsystems 10 Future Development Directions Part III - Case Studies C A S E S T U D I E S 11 Bionic Tracking: Using Eye Tracking for Cell Tracking 12 Towards Interactive Virtual Reality Laser Ablation 13 Rendering the Adaptive Particle Representation 14 sciview — Integrating scenery into ImageJ2 & Fiji Part IV - Conclusion 15 Conclusions and Outlook Backmatter & Appendices A Questionnaire for VR Ablation User Study B Full Correlations in VR Ablation Questionnaire C Questionnaire for Bionic Tracking User Study List of Tables List of Figures Bibliography Selbstständigkeitserklärun

    Adaptive beam control and analysis in fluorescence microscopy

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    This thesis details three novel advances in instrumentation that are each related to performance improvement in wide-field visible-spectrum imaging systems. In each case our solution concerns the assessment and improvement of optical imaging quality. The three instruments are as follows: The first is a portable transmission microscope which is able to correct for artificially induced aberrations using adaptive optics (AO). The specimens and the method of introducing aberrations into the optical system can be altered to simulate the performance of AO-correction in both astronomical and biological imaging. We present the design and construction of the system alongside before-and-after AO-correction images for simulated astronomical and biological images. The second instrument is a miniature endoscope camera sensor we re-purposed for use as a quantitative beam analysis probe using a custom high dynamic range (HDR) imaging and reconstruction procedure. This allowed us to produce quantitative flux maps of the illumination beam intensity profile within several operational fluorescence microscope systems. The third and final project in this thesis was concerned with an adaptive modification to the light sheet illumination beam used in light sheet microscopy, specifically for a single plane illumination microscope (SPIM), embracing the trade-off between the thickness of the light sheet and its extent across the detection field-of-view. The focal region of the beam was made as small as possible and then matched to the shape of curved features within a biological specimen by using a spatial light modulator (SLM) to alter the light sheet focal length throughout the vertical span of the sheet. We used the HDR beam profiling camera probe mentioned earlier to assess the focal shape and quality of the beam. The resulting illumination beam may in the future be used in a modified SPIM system to produce fluorescence microscope images with enhanced optical sectioning of specific curved features

    Field-portable pixel super-resolution colour microscope.

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    Based on partially-coherent digital in-line holography, we report a field-portable microscope that can render lensfree colour images over a wide field-of-view of e.g., >20 mm(2). This computational holographic microscope weighs less than 145 grams with dimensions smaller than 17Ă—6Ă—5 cm, making it especially suitable for field settings and point-of-care use. In this lensfree imaging design, we merged a colorization algorithm with a source shifting based multi-height pixel super-resolution technique to mitigate 'rainbow' like colour artefacts that are typical in holographic imaging. This image processing scheme is based on transforming the colour components of an RGB image into YUV colour space, which separates colour information from brightness component of an image. The resolution of our super-resolution colour microscope was characterized using a USAF test chart to confirm sub-micron spatial resolution, even for reconstructions that employ multi-height phase recovery to handle dense and connected objects. To further demonstrate the performance of this colour microscope Papanicolaou (Pap) smears were also successfully imaged. This field-portable and wide-field computational colour microscope could be useful for tele-medicine applications in resource poor settings

    4Pi live cell imaging

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    One distinctive advantage of light microscopy over electron microscopy is it ability to selectively image sub-cellular details three-dimensionally in living cells. Live cell imaging is the domain of light microscopy. In this thesis a live cell imaging setup relying on 4Pi fluorescence microscopy is presented. To speed up the imaging process and record cellular processes of the order of a few seconds a new method of multifoci-generation via the stacking of birefringent crystals is implemented. The axial optical sectioning ability of the system is ~120 nm and the recording of an average-sized 3D data stack is accomplished in less than 10 seconds. The microscope’s applicability to live cell imaging is verified by recording both mitochondrial fusion and fission events in live yeast and the movement of PML bodies in live human U2OS cells. To push the limits of applicability of the system further, second harmonic generation is tested as an alternative label-free coherent contrast mechanism and binary amplitude filters are successfully applied. Second harmonic generation turns out to be an imaging technique confined to specific applications. With the implementation of amplitude filters 4Pi microscopy of aqueous tissue becomes convenient and broadly applicable

    Modeling and Simulation in Engineering

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    This book provides an open platform to establish and share knowledge developed by scholars, scientists, and engineers from all over the world, about various applications of the modeling and simulation in the design process of products, in various engineering fields. The book consists of 12 chapters arranged in two sections (3D Modeling and Virtual Prototyping), reflecting the multidimensionality of applications related to modeling and simulation. Some of the most recent modeling and simulation techniques, as well as some of the most accurate and sophisticated software in treating complex systems, are applied. All the original contributions in this book are jointed by the basic principle of a successful modeling and simulation process: as complex as necessary, and as simple as possible. The idea is to manipulate the simplifying assumptions in a way that reduces the complexity of the model (in order to make a real-time simulation), but without altering the precision of the results
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