Modeling, Pattern Analysis and Feature-Based Retrieval on Retinal Images

Inexpensive high quality fundus camera systems enable imaging of retina for vision related health management and diagnosis at large scale. A computer based analysis system can help establish the general baseline of normal conditions vs. anomalous ones, so that different classes of retinal conditions can be classified. Advanced applications, ranging from disease screening algorithms, aging vs. disease trend modeling and prediction, and content-based retrieval systems can be developed. In this dissertation, I propose an analytical framework for the modeling of retina blood vessels to capture their statistical properties, so that based on these properties one can develop blood vessel mapping algorithms with self-optimized parameters. Then, other image objects can be registered based on vascular topology modeling techniques. On the basis of these low level analytical models and algorithms, the third major element of this dissertation is a high level population statistics application, in which texture classification of macular patterns is correlated with vessel structures, which can also be used for retinal image retrieval. The analytical models have been implemented and tested based on various image sources. Some of the algorithms have been used for clinical tests. The major contributions of this dissertation are summarized as follows: (1) A concise, accurate feature representation of retinal blood vessel on retinal images by proposing two feature descriptors Sp and Ep derived from radial contrast transform. (2) A new statistical model of lognormal distribution, which captures the underlying physical property of the levels of generations of the vascular network on retinal images. (3) Fast and accurate detection algorithms for retinal objects, which include retinal blood vessel, macular-fovea area and optic disc, and (4) A novel population statistics based modeling technique for correlation analysis of blood vessels and other image objects that only exhibit subtle texture changes

Multimodal retinal imaging: Improving accuracy and efficiency of image registration using Mutual Information

This thesis addresses the challenging task of multi-modal image registration. Registration is often required in a number of applications, whereby two images are aligned to give matching correspondence between the features in each image. Such techniques have become popular in many different fields, especially in medical imaging. Multi-modal registration would allow for anatomical structure to be studied concurrently in both modalities, providing the clinician with a greater insight of the patient's condition. Glaucoma is a serious condition that damages the optic nerve progressively, leading to irreversible blindness. The disease can be treated so to prevent any further infection, however it can not be reversed. Therefore it is paramount that the disease is detected in the early stages so to minimise the affect of the condition. The work in this thesis focuses on two particular imaging modalities: colour fundus photographs and scanning laser ophthalmoscope images. Both images are captured from the human eye and show the appearance and reflectivity of the retina respectively. Registration of these two modalities would significantly improve demarcation and monitoring of the optic nerve head, a crucial stage for glaucoma diagnosis. In recent years, Mutual Information has become a popular technique used to perform multi-modal registration. This thesis provides a comprehensive overview of the algorithm. Firstly, an investigation is performed that shows how probability estimation can improve the algorithm performance. Secondly, the weaknesses of the current technique are revealed and so a novel solution is proposed that overcomes these problems. Finally, the proposed solution is incorporated in a non-rigid registration scheme that provides excellent registration accuracy for our intended application

The 2017 Magnetism Roadmap

Building upon the success and relevance of the 2014 Magnetism Roadmap, this 2017 Magnetism Roadmap edition follows a similar general layout, even if its focus is naturally shifted, and a different group of experts and, thus, viewpoints are being collected and presented. More importantly, key developments have changed the research landscape in very relevant ways, so that a novel view onto some of the most crucial developments is warranted, and thus, this 2017 Magnetism Roadmap article is a timely endeavour. The change in landscape is hereby not exclusively scientific, but also reflects the magnetism related industrial application portfolio. Specifically, Hard Disk Drive technology, which still dominates digital storage and will continue to do so for many years, if not decades, has now limited its footprint in the scientific and research community, whereas significantly growing interest in magnetism and magnetic materials in relation to energy applications is noticeable, and other technological fields are emerging as well. Also, more and more work is occurring in which complex topologies of magnetically ordered states are being explored, hereby aiming at a technological utilization of the very theoretical concepts that were recognised by the 2016 Nobel Prize in Physics. Given this somewhat shifted scenario, it seemed appropriate to select topics for this Roadmap article that represent the three core pillars of magnetism, namely magnetic materials, magnetic phenomena and associated characterization techniques, as well as applications of magnetism. While many of the contributions in this Roadmap have clearly overlapping relevance in all three fields, their relative focus is mostly associated to one of the three pillars. In this way, the interconnecting roles of having suitable magnetic materials, understanding (and being able to characterize) the underlying physics of their behaviour and utilizing them for applications and devices is well illustrated, thus giving an accurate snapshot of the world of magnetism in 2017. The article consists of 14 sections, each written by an expert in the field and addressing a specific subject on two pages. Evidently, the depth at which each contribution can describe the subject matter is limited and a full review of their statuses, advances, challenges and perspectives cannot be fully accomplished. Also, magnetism, as a vibrant research field, is too diverse, so that a number of areas will not be adequately represented here, leaving space for further Roadmap editions in the future. However, this 2017 Magnetism Roadmap article can provide a frame that will enable the reader to judge where each subject and magnetism research field stands overall today and which directions it might take in the foreseeable future. The first material focused pillar of the 2017 Magnetism Roadmap contains five articles, which address the questions of atomic scale confinement, 2D, curved and topological magnetic materials, as well as materials exhibiting unconventional magnetic phase transitions. The second pillar also has five contributions, which are devoted to advances in magnetic characterization, magneto-optics and magneto-plasmonics, ultrafast magnetization dynamics and magnonic transport. The final and application focused pillar has four contributions, which present non-volatile memory technology, antiferromagnetic spintronics, as well as magnet technology for energy and bio-related applications. As a whole, the 2017 Magnetism Roadmap article, just as with its 2014 predecessor, is intended to act as a reference point and guideline for emerging research directions in modern magnetism

The Boston University Photonics Center annual report 2005-2006

This repository item contains an annual report that summarizes activities of the Boston University Photonics Center in the 2005-2006 academic year. The report provides quantitative and descriptive information regarding photonics programs in education, interdisciplinary research, business innovation, and technology development. The Boston University Photonics Center (BUPC) is an interdisciplinary hub for education, research, scholarship, innovation, and technology development associated with practical uses of light.This Annual Report is intended to serve as a synopsis of the Boston University Photonics Center’s wide-ranging activities for the period from July 2005 through June 2006, corresponding to the University’s fiscal year. It is my hope that the document is reflective of the Center’s core values in innovation, entrepreneurship, and education, and that it projects our shared vision, and our dedication to excellence in this exciting field. For further information, you may visit our new website at www.bu.edu/photonics. Though only recently appointed as Director, my involvement in Center activities dates back to the Center’s formation more than ten years ago. In the early years, I worked with a team of faculty and staff colleagues to design and construct the shared laboratories that now provide every Center member extraordinary capabilities for fabrication and testing of advanced photonic devices and systems. I helped launch the business incubator by forming a company around an idea that emerged from my research laboratory. While that company failed to realize its vision of transforming the compact disc industry, it did help us form a unique vision for our program of academically engaged business acceleration. I co-developed a course in optical microsystems for telecommunications that I taught to advanced undergraduates and graduate students in the new M.S. degree program in Photonics offered through the Electrical and Computer Engineering Department. And since the Center’s inception, I have contributed to its scholarly mission through my work in optical microsystem design and precision manufacturing at the Center’s core Precision Engineering Research Laboratory. Recently, I had the opportunity to lead the Provost’s Faculty Advisory Committee on Photonics, charged with broadening the Center’s mission to better integrate academic and educational programs with its more established programs for business incubation and prototype development. [TRUNCATED

Annual Report 2019 - Institute of Ion Beam Physics and Materials Research

The Institute of Ion Beam Physics and Materials Research conducts materials research for future applications in, e.g., information technology. To this end, we make use of the various possibilities offered by our Ion Beam Center (IBC) for synthesis, modification, and analysis of thin films and nanostructures, as well as of the free-electron laser FELBE at HZDR for THz spectroscopy. The analyzed materials range from semiconductors and oxides to metals and magnetic materials. They are investigated with the goal to optimize their electronic, magnetic, optical as well as structural functionality. This research is embedded in the Helmholtz Association’s programme “From Matter to Materials and Life”. Seven publications from last year are highlighted in this Annual Report to illustrate the wide scientific spectrum of our institute. After the scientific evaluation in the framework of the Helmholtz Programme-Oriented Funding (POF) in 2018 we had some time to concentrate on science again before end of the year a few of us again had to prepare for the strategic evaluation which took place in January 2020, which finally was also successful for the Institute

A novel Automatic Optic Disc and Cup Image Segmentation System for Diagnosing Glaucoma using RIGA dataset

The optic nerve head (ONH) of the retina is a very important landmark of the fundus and is altered in optic nerve pathology especially glaucoma. Numerous imaging systems are available to capture the retinal fundus and from which some structural parameters can be inferred the retinal fundus camera is one of the most important tools used for this purpose. Currently, the ONH structure examination of the fundus images is conducted by the professionals only by observation. It should be noted that there is a shortage of highly trained professional worldwide. Therefore a reliable and efficient optic disc and cup localization and segmentation algorithms are important for automatic eye disease screening and also for monitoring the progression/remission of the disease Thus in order to develop a system, a retinal fundus image dataset is necessary to train and test the new software systems. The methods for diagnosing glaucoma are reviewed in the first chapter. Various datasets of retinal fundus images that are publically available currently are described and discussed. In the second chapter the techniques for the optic disc and cup segmentations available in the literature is reviewed. While in the third chapter a unique retinal fundus image dataset, called RIGA (retinal images for glaucoma analysis) is presented. In the dataset, the optic disc and cup boundaries are annotated manually by 6 ophthalmologists (glaucoma professionals) independently for total of 4500 images in order to obtain a comprehensive view point as well as to see the variation and agreement between these professionals. Based upon these evaluations, some of the images were filtered based on a statistical analysis in order to increase the reliability. The new optic disc and cup segmentation methodologies are discussed in the fourth chapter. The process starts with a preprocessing step based on a reliable and precise algorithm. Here an Interval Type-II fuzzy entropy based thresholding scheme along with Differential Evolution was applied to determine the location of the optic disc in order to determine the region of interest instead of dealing with the entire image. Then, the processing step is discussed. Two algorithms were applied: one for optic disc segmentation based on an active contour model implemented by level set approach, and the second for optic cup segmentation. For this thresholding was applied to localize the disc. The disc and cup area and centroid are then calculated in order to evaluate them based on the manual annotations of areas and centroid for the filtered images based on the statistical analysis. In the fifth chapter, after segmenting the disc and cup, the clinical parameters in diagnosis of glaucoma such as horizontal and vertical cup to disc ratio (HCDR) and (VCDR) are computed automatically as a post processing step in order to compare the results with the six ophthalmologist’s manual annotations results. The thesis is concluded in chapter six with discussion of future plans

Optic disc detection in video sequences from video ophthalmoscope

Tato práce je zaměřena na automatickou detekci optického disku v sítnicových obrazech. Je zde stručně popsána anatomie lidského oka, principy snímání očního pozadí a také přehled používaných metod pro detekci optického disku. Praktická část popisuje vytvořené postupy pro detekci optického disku, tedy detekci založenou na metodě rozvodí, aktivních konturách a také na metodě narůstání oblastí. Stěžejní metodou této práce je metoda kruhové transformace, která jako jediná umožnila detekovat optický disk na snímcích z video oftalmoskopu a také na kvalitních snímcích z fundus kamer. Metoda kruhové transformace byla otestována na třech databázích. Na databázi HRF dosáhla průměrného překrytí 92,44 %, na databázi DRIONS 91,03 % a na snímcích z video oftalmoskopu pak 77,36 %.This work is focused on automatic detection of optic disc in retinal images. There is briefly described anatomy of human eye, principles of retinal imaging and also overview of the methods used for optic disc detection. The practical part describes developed procedures for optic disc detection, ie detection based on watershed transform, active contours and also on region growing technique. The main method of this work is the method of circular transformation, which as the only one allowed to detect the optic disc on the images of video ophtalmoscope and also on the high quality images from fundus cameras. This method was tested on three datasets. The average overlap 92,44 % was achieved for HRF dataset, 91,03 for DRIONS dataset and 77,36 for images of video ophtalmoscope.

Properties of Synaptic Transmission from Rods and Cones in The Outer Plexiform Layer of The Vertebrate Retina

Photoreceptors are the first neurons in the visual system. They transduce changes in light intensity into graded changes in membrane potential that are then transformed into chemical signals by regulating the release of glutamate-filled synaptic vesicles. Rod and cone photoreceptors release glutamate continuously in darkness and release slows in light. To help track rapid changes in light intensity, photoreceptors are capable of both rapid exocytosis and rapid endocytosis of synaptic vesicles. Endocytosis is needed for recycling synaptic vesicles but also appears to be important for removing proteins and lipids from active zones to restore release site function after prior vesicle fusion. Synaptic exocytosis from vertebrate photoreceptors involves synaptic ribbons that cluster vesicles near the presynaptic membrane. We hypothesized that such clustering increases the likelihood that exocytosis at one ribbon release site may disrupt release at an adjacent site. Consistent with this, studies described in Chapter 2 showed that endocytosis is needed to rapidly restore release site competence at photoreceptor ribbon synapses. We combined optical and electrophysiological techniques to show that endocytosis is important for restoring late steps in the vesicle fusion process but does not appear to be needed for vesicles to dock successfully at the membrane. Release site clearance by endocytosis is thus essential for continuous release in photoreceptors. We explore mechanisms that contribute to efficient synaptic vesicle exocytosis and endocytosis in Chapter 3. Exocytosis and endocytosis of synaptic vesicles can be coupled in two general ways. In the full-collapse model, the vesicle membrane merges completely with the plasma membrane and so vesicles must be fully reconstructed before they can be retrieved by endocytosis. In the kiss-and-run model, a vesicle briefly contacts the plasma membrane through a small fusion pore that permits release of small molecules but the vesicle does not flatten into the plasma membrane. The vesicle with its complement of proteins is quickly recycled to the cytoplasm after closure of the fusion pore during kiss-and-run. Using a combination of techniques including total internal reflectance fluorescence microscopy (TIRFM), confocal microscopy, electron microscopy, and membrane capacitance measurements, we found that kiss-and-run exocytosis and endocytosis contributes to more than 50% of the release events in photoreceptors. In addition to speeding endocytosis, kiss-and-run fusion may limit disruption of release site structure during fusion, providing an efficient mechanism to facilitate sustained release. HCs not only receive excitatory feedforward signals from photoreceptors, but also send inhibitory feedback signals back to photoreceptors. At normal physiological membrane potentials in cones, inhibitory feedback from HCs to cones increases the activity of L-type voltage-gated Ca2+ channels producing inward feedback currents that increase the synaptic release of glutamate. In the final chapter of this thesis, we describe studies using paired whole cell recordings to determine if, in addition to Ca2+ currents, other currents also contribute to these inward feedback currents in cones. We found that feedback currents in cones involve a smaller than expected contribution from Ca2+-activated Cl- currents and a larger than expected contribution from Cl- currents associated with glutamate transporter activity in cones