NiftyNet: a deep-learning platform for medical imaging

Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this application requires substantial implementation effort. Thus, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. NiftyNet provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on TensorFlow and supports TensorBoard visualization of 2D and 3D images and computational graphs by default. We present 3 illustrative medical image analysis applications built using NiftyNet: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. NiftyNet enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications.Comment: Wenqi Li and Eli Gibson contributed equally to this work. M. Jorge Cardoso and Tom Vercauteren contributed equally to this work. 26 pages, 6 figures; Update includes additional applications, updated author list and formatting for journal submissio

Cognitive visual tracking and camera control

Cognitive visual tracking is the process of observing and understanding the behaviour of a moving person. This paper presents an efficient solution to extract, in real-time, high-level information from an observed scene, and generate the most appropriate commands for a set of pan-tilt-zoom (PTZ) cameras in a surveillance scenario. Such a high-level feedback control loop, which is the main novelty of our work, will serve to reduce uncertainties in the observed scene and to maximize the amount of information extracted from it. It is implemented with a distributed camera system using SQL tables as virtual communication channels, and Situation Graph Trees for knowledge representation, inference and high-level camera control. A set of experiments in a surveillance scenario show the effectiveness of our approach and its potential for real applications of cognitive vision

Semantic Image Retrieval via Active Grounding of Visual Situations

We describe a novel architecture for semantic image retrieval---in particular, retrieval of instances of visual situations. Visual situations are concepts such as "a boxing match," "walking the dog," "a crowd waiting for a bus," or "a game of ping-pong," whose instantiations in images are linked more by their common spatial and semantic structure than by low-level visual similarity. Given a query situation description, our architecture---called Situate---learns models capturing the visual features of expected objects as well the expected spatial configuration of relationships among objects. Given a new image, Situate uses these models in an attempt to ground (i.e., to create a bounding box locating) each expected component of the situation in the image via an active search procedure. Situate uses the resulting grounding to compute a score indicating the degree to which the new image is judged to contain an instance of the situation. Such scores can be used to rank images in a collection as part of a retrieval system. In the preliminary study described here, we demonstrate the promise of this system by comparing Situate's performance with that of two baseline methods, as well as with a related semantic image-retrieval system based on "scene graphs.

Neurocognitive Informatics Manifesto.

Informatics studies all aspects of the structure of natural and artificial information systems. Theoretical and abstract approaches to information have made great advances, but human information processing is still unmatched in many areas, including information management, representation and understanding. Neurocognitive informatics is a new, emerging field that should help to improve the matching of artificial and natural systems, and inspire better computational algorithms to solve problems that are still beyond the reach of machines. In this position paper examples of neurocognitive inspirations and promising directions in this area are given

Knowledge-based support in Non-Destructive Testing for health monitoring of aircraft structures

Maintenance manuals include general methods and procedures for industrial maintenance and they contain information about principles of maintenance methods. Particularly, Non-Destructive Testing (NDT) methods are important for the detection of aeronautical defects and they can be used for various kinds of material and in different environments. Conventional non-destructive evaluation inspections are done at periodic maintenance checks. Usually, the list of tools used in a maintenance program is simply located in the introduction of manuals, without any precision as regards to their characteristics, except for a short description of the manufacturer and tasks in which they are employed. Improving the identification concepts of the maintenance tools is needed to manage the set of equipments and establish a system of equivalence: it is necessary to have a consistent maintenance conceptualization, flexible enough to fit all current equipment, but also all those likely to be added/used in the future. Our contribution is related to the formal specification of the system of functional equivalences that can facilitate the maintenance activities with means to determine whether a tool can be substituted for another by observing their key parameters in the identified characteristics. Reasoning mechanisms of conceptual graphs constitute the baseline elements to measure the fit or unfit between an equipment model and a maintenance activity model. Graph operations are used for processing answers to a query and this graph-based approach to the search method is in-line with the logical view of information retrieval. The methodology described supports knowledge formalization and capitalization of experienced NDT practitioners. As a result, it enables the selection of a NDT technique and outlines its capabilities with acceptable alternatives

Design of testbed and emulation tools

The research summarized was concerned with the design of testbed and emulation tools suitable to assist in projecting, with reasonable accuracy, the expected performance of highly concurrent computing systems on large, complete applications. Such testbed and emulation tools are intended for the eventual use of those exploring new concurrent system architectures and organizations, either as users or as designers of such systems. While a range of alternatives was considered, a software based set of hierarchical tools was chosen to provide maximum flexibility, to ease in moving to new computers as technology improves and to take advantage of the inherent reliability and availability of commercially available computing systems