3D-surface reconstruction of cellular cryo-soft X-ray microscopy tomograms using semi-supervised deep learning

Cryo-soft X-ray tomography (cryo-SXT) is a powerful method to investigate the ultrastructure of cells, offering resolution in the tens of nm range and strong contrast for membranous structures without requirement for labeling or chemical fixation. The short acquisition time and the relatively large volumes acquired allow for fast acquisition of large amounts of tomographic image data. Segmentation of these data into accessible features is a necessary step in gaining biologically relevant information from cryo-soft X-ray tomograms. However, manual image segmentation still requires several orders of magnitude more time than data acquisition. To address this challenge, we have here developed an end-to-end automated 3D-segmentation pipeline based on semi-supervised deep learning. Our approach is suitable for high-throughput analysis of large amounts of tomographic data, while being robust when faced with limited manual annotations and variations in the tomographic conditions. We validate our approach by extracting three-dimensional information on cellular ultrastructure and by quantifying nanoscopic morphological parameters of filopodia in mammalian cells

AI/ML Algorithms and Applications in VLSI Design and Technology

An evident challenge ahead for the integrated circuit (IC) industry in the nanometer regime is the investigation and development of methods that can reduce the design complexity ensuing from growing process variations and curtail the turnaround time of chip manufacturing. Conventional methodologies employed for such tasks are largely manual; thus, time-consuming and resource-intensive. In contrast, the unique learning strategies of artificial intelligence (AI) provide numerous exciting automated approaches for handling complex and data-intensive tasks in very-large-scale integration (VLSI) design and testing. Employing AI and machine learning (ML) algorithms in VLSI design and manufacturing reduces the time and effort for understanding and processing the data within and across different abstraction levels via automated learning algorithms. It, in turn, improves the IC yield and reduces the manufacturing turnaround time. This paper thoroughly reviews the AI/ML automated approaches introduced in the past towards VLSI design and manufacturing. Moreover, we discuss the scope of AI/ML applications in the future at various abstraction levels to revolutionize the field of VLSI design, aiming for high-speed, highly intelligent, and efficient implementations

(I123)FP-CIT reporting: Machine Learning, Effectiveness and Clinical Integration

(I123)FP-CIT imaging is used for differential diagnosis of clinically uncertain Parkinsonian Syndromes. Conventional reporting relies on visual interpretation of images and analysis of semi-quantification results. However, this form of reporting is associated with variable diagnostic accuracy results. The first half of this thesis clarifies whether machine learning classification algorithms, used as computer aided diagnosis (CADx) tool, can offer improved performance. Candidate machine learning classification algorithms were developed and compared to a range of semi-quantitative methods, which showed the superiority of machine learning tools in terms of binary classification performance. The best of the machine learning algorithms, based on 5 principal components and a linear Support Vector Machine classifier, was then integrated into clinical software for a reporting exercise (pilot and main study). Results demonstrated that the CADx software had a consistently high standalone accuracy. In general, CADx caused reporters to give more consistent decisions and resulted in improved diagnostic accuracy when viewing images with unfamiliar appearances. However, although these results were undoubtedly impressive, it was also clear that a number of additional, significant hurdles remained, that needed to be overcome before widespread clinical adoption could be achieved. Consequently, the second half of this thesis focuses on addressing one particular aspect of the remaining translation gap for (I123)FP-CIT classification software, namely heterogeneity of the clinical environment. Introduction of new technology, such as machine learning, may require new metrics, which in this work were informed through novel methods (such as the use of innovative phantoms) and strategies, enabling sensitivity testing to be developed, applied and evaluated. The pathway to acceptance of novel and progressive technology in the clinic is a tortuous one, and this thesis emphasises the importance of many factors in addition to the core technology that need to be addressed if such tools are ever to achieve clinical adoption

Optimisation of Positron Emission Tomography based target volume delineation in head and neck radiotherapy

Automatic segmentation of tumours using Positron Emission Tomography (PET) was recommended for radiotherapy treatment (RT) planning of head and neck (H&N) cancer patients, and investigated in the scientific literature without reaching a consensus on the optimal process. This project aimed at evaluating the performance of PETCbased automatic segmentation (PETCAS) methods and developing an optimal PETC AS process to be used at Velindre Cancer Centre (VCC). For this purpose, ten algorithms were implemented to represent the most promising PETCAS approaches from a systematic review of the literature. The algorithms’ performance was evaluated on filled phantom inserts with variable size, geometry, tumour intensity and image noise. The impact of thick insert plastic walls on both image quantification and segmentation was thoroughly assessed. The PETCAS methods were further applied to realistic H&N tumours, modelled using a printed subresolution sandwich phantom developed and calibrated in house. Results showed that different PETCAS performed best for different types of target objects. An Advanced decision TreeCbased Learning Algorithm for Automatic Segmentation (ATLAAS) was therefore developed and validated for the selection of the optimal PETCAS approach according to the target object characteristics. Finally, a protocol was designed for the use of PETCAS within RT planning at VCC. The protocol was used retrospectively on a group of 10 oropharyngeal cancer patients, and the results highlighted the additional information brought by PET beyond anatomical imaging. In a prospective study on 10 additional patients, PETCAS replaced manual PET/CT delineation, and accounted for up to 33% of the modifications of manually drawn CT/MRI contours to derive the final planning contour. This study demonstrated the usefulness and reliability of the PETCAS method in RT planning, and led to modifying the clinical workflow for H&N patients at VCC. This work has the potential to be extended to other tumour sites and institutions

Earth Resources: A continuing bibliography (issue 32)

This bibliography list 580 reports, articles and other documents introduced into the NASA scientific and technical information system. Emphasis is placed on the use of remote sensing and geophysical instrumentation in spacecraft and aircraft to survey and inventory natural resources and urban areas. Subject matter is grouped according to agriculture and forestry, environmental changes and cultural resources, geodesy and cartography, geology and mineral resources, hydrology and water management, data processing and distribution systems, instrumentation and sensors, and economic analysis

SSERVI Annual Report: Year 4

The SSERVI Central Office forms the organizational, administrative and collaborative hub for the domestic and international teams, and is responsible for advocacy and ensuring the long-term health and relevance of the Institute. SSERVI has increased the cross-talk between NASAs space and human exploration programs, which is one of our primary goals. We bring multidisciplinary teams together to address fundamental and strategic questions pertinent to future human space exploration, and the results from that research are the primary products of the institute. The team and international partnership reports contain summaries of 2017 research accomplishments. Here we present the 2017 accomplishments by the SSERVI Central Office that focus on: 1) Supporting Our Teams, 2) Community Building, 3) Managing the Solar System Treks Portal (SSTP), and 4) Public Engagement