Information technology applications in biomedical functional imaging

Author name used in this publication: (David) Dagan FengCentre for Multimedia Signal Processing, Department of Electronic and Information EngineeringVersion of RecordPublishe

Dynamic image data compression in spatial and temporal domains : theory and algorithm

Author name used in this publication: Dagan FengVersion of RecordPublishe

Energy Consumption Of Visual Sensor Networks: Impact Of Spatio-Temporal Coverage

Wireless visual sensor networks (VSNs) are expected to play a major role in future IEEE 802.15.4 personal area networks (PAN) under recently-established collision-free medium access control (MAC) protocols, such as the IEEE 802.15.4e-2012 MAC. In such environments, the VSN energy consumption is affected by the number of camera sensors deployed (spatial coverage), as well as the number of captured video frames out of which each node processes and transmits data (temporal coverage). In this paper, we explore this aspect for uniformly-formed VSNs, i.e., networks comprising identical wireless visual sensor nodes connected to a collection node via a balanced cluster-tree topology, with each node producing independent identically-distributed bitstream sizes after processing the video frames captured within each network activation interval. We derive analytic results for the energy-optimal spatio-temporal coverage parameters of such VSNs under a-priori known bounds for the number of frames to process per sensor and the number of nodes to deploy within each tier of the VSN. Our results are parametric to the probability density function characterizing the bitstream size produced by each node and the energy consumption rates of the system of interest. Experimental results reveal that our analytic results are always within 7% of the energy consumption measurements for a wide range of settings. In addition, results obtained via a multimedia subsystem show that the optimal spatio-temporal settings derived by the proposed framework allow for substantial reduction of energy consumption in comparison to ad-hoc settings. As such, our analytic modeling is useful for early-stage studies of possible VSN deployments under collision-free MAC protocols prior to costly and time-consuming experiments in the field.Comment: to appear in IEEE Transactions on Circuits and Systems for Video Technology, 201

Master Texture Space: An Efficient Encoding for Projectively Mapped Objects

Projectively textured models are used in an increasingly large number of applicationsthat dynamically combine images with a simple geometric surface in a viewpoint dependentway. These models can provide visual fidelity while retaining the effects affordedby geometric approximation such as shadow casting and accurate perspective distortion.However, the number of stored views can be quite large and novel views must be synthesizedduring the rendering process because no single view may correctly texture the entireobject surface. This work introduces the Master Texture encoding and demonstrates thatthe encoding increases the utility of projectively textured objects by reducing render-timeoperations. Encoding involves three steps; 1) all image regions that correspond to the samegeometric mesh element are extracted and warped to a facet of uniform size and shape,2) an efficient packing of these facets into a new Master Texture image is computed, and3) the visibility of each pixel in the new Master Texture data is guaranteed using a simplealgorithm to discard occluded pixels in each view. Because the encoding implicitly representsthe multi-view geometry of the multiple images, a single texture mesh is sufficientto render the view-dependent model. More importantly, every Master Texture image cancorrectly texture the entire surface of the object, removing expensive computations suchas visibility analysis from the rendering algorithm. A benefit of this encoding is the supportfor pixel-wise view synthesis. The utility of pixel-wise view synthesis is demonstratedwith a real-time Master Texture encoded VDTM application. Pixel-wise synthesis is alsodemonstrated with an algorithm that distills a set of Master Texture images to a singleview-independent Master Texture image

Quantum-Assisted Learning of Hardware-Embedded Probabilistic Graphical Models

Mainstream machine-learning techniques such as deep learning and probabilistic programming rely heavily on sampling from generally intractable probability distributions. There is increasing interest in the potential advantages of using quantum computing technologies as sampling engines to speed up these tasks or to make them more effective. However, some pressing challenges in state-of-the-art quantum annealers have to be overcome before we can assess their actual performance. The sparse connectivity, resulting from the local interaction between quantum bits in physical hardware implementations, is considered the most severe limitation to the quality of constructing powerful generative unsupervised machine-learning models. Here we use embedding techniques to add redundancy to data sets, allowing us to increase the modeling capacity of quantum annealers. We illustrate our findings by training hardware-embedded graphical models on a binarized data set of handwritten digits and two synthetic data sets in experiments with up to 940 quantum bits. Our model can be trained in quantum hardware without full knowledge of the effective parameters specifying the corresponding quantum Gibbs-like distribution; therefore, this approach avoids the need to infer the effective temperature at each iteration, speeding up learning; it also mitigates the effect of noise in the control parameters, making it robust to deviations from the reference Gibbs distribution. Our approach demonstrates the feasibility of using quantum annealers for implementing generative models, and it provides a suitable framework for benchmarking these quantum technologies on machine-learning-related tasks.Comment: 17 pages, 8 figures. Minor further revisions. As published in Phys. Rev.

Segmentation of dynamic PET images using cluster analysis

Author name used in this publication: Dagan FengVersion of RecordPublishe

Geobase Information System Impacts on Space Image Formats

As Geobase Information Systems increase in number, size and complexity, the format compatability of satellite remote sensing data becomes increasingly more important. Because of the vast and continually increasing quantity of data available from remote sensing systems the utility of these data is increasingly dependent on the degree to which their formats facilitate, or hinder, their incorporation into Geobase Information Systems. To merge satellite data into a geobase system requires that they both have a compatible geographic referencing system. Greater acceptance of satellite data by the user community will be facilitated if the data are in a form which most readily corresponds to existing geobase data structures. The conference addressed a number of specific topics and made recommendations

Acceleration of GATE Monte Carlo simulations

Positron Emission Tomography (PET) and Single Photon Emission Computed Tomography are forms of medical imaging that produce functional images that reflect biological processes. They are based on the tracer principle. A biologically active substance, a pharmaceutical, is selected so that its spatial and temporal distribution in the body reflects a certain body function or metabolism. In order to form images of the distribution, the pharmaceutical is labeled with gamma-ray-emitting or positron-emitting radionuclides (radiopharmaceuticals or tracers). After administration of the tracer to a patient, an external position-sensitive gamma-ray camera can detect the emitted radiation to form a stack of images of the radionuclide distribution after a reconstruction process. Monte Carlo methods are numerical methods that use random numbers to compute quantities of interest. This is normally done by creating a random variable whose expected value is the desired quantity. One then simulates and tabulates the random variable and uses its sample mean and variance to construct probabilistic estimates. It represents an attempt to model nature through direct simulation of the essential dynamics of the system in question. Monte Carlo modeling is the method of choice for all applications where measurements are not feasible or where analytic models are not available due to the complex nature of the problem. In addition, such modeling is a practical approach in nuclear medical imaging in several important application fields: detector design, quantification, correction methods for image degradations, detection tasks etc. Several powerful dedicated Monte Carlo simulators for PET and/or SPECT are available. However, they are often not detailed nor flexible enough to enable realistic simulations of emission tomography detector geometries while also modeling time dependent processes such as decay, tracer kinetics, patient and bed motion, dead time or detector orbits. Our Monte Carlo simulator of choice, GEANT4 Application for Tomographic Emission (GATE), was specifically designed to address all these issues. The flexibility of GATE comes at a price however. The simulation of a simple prototype SPECT detector may be feasible within hours in GATE but an acquisition with a realistic phantom may take years to complete on a single CPU. In this dissertation we therefore focus on the Achilles’ heel of GATE: efficiency. Acceleration of GATE simulations can only be achieved through a combination of efficient data analysis, dedicated variance reduction techniques, fast navigation algorithms and parallelization. In the first part of this dissertation we consider the improvement of the analysis capabilities of GATE. The static analysis module in GATE is both inflexible and incapable of storing more detail without introducing a large computational overhead. However, the design and validation of the acceleration techniques in this dissertation requires a flexible, detailed and computationally efficient analysis module. To this end, we develop a new analysis framework capable of analyzing any process, from the decay of isotopes to particle interactions and detections in any detector element for any type of phantom. The evaluation of our framework consists of the assessment of spurious activity in 124I-Bexxar PET and of contamination in 131I-Bexxar SPECT. In the case of PET we describe how our framework can detect spurious coincidences generated by non-pure isotopes, even with realistic phantoms. We show that optimized energy thresholds, which can readily be applied in the clinic, can now be derived in order to minimize the contamination. We also show that the spurious activity itself is not spatially uniform. Therefore standard reconstruction and correction techniques are not adequate. In the case of SPECT we describe how it is now possible to classify detections into geometric detections, phantom scatter, penetration through the collimator, collimator scatter and backscatter in the end parts. We show that standard correction algorithms such as triple energy window correction cannot correct for septal penetration. We demonstrate that 124I PET with optimized energy thresholds offer better image quality than 131I SPECT when using standard reconstruction techniques. In the second part of this dissertation we focus on improving the efficiency of GATE with a variance reduction technique called Geometrical Importance Sampling (GIS). We describe how only 0.02% of all emitted photons can reach the crystal surface of a SPECT detector head with a low energy high resolution collimator. A lot of computing power is therefore wasted by tracking photons that will not contribute to the result. A twofold strategy is used to solve this problem: GIS employs Russian Roulette to discard those photons that will not likely contribute to the result. Photons in more important regions on the other hand are split into several photons with reduced weight to increase their survival chance. We show that this technique introduces branches into the particle history. We describe how this can be taken into account by a particle history tree that is used for the analysis of the results. The evaluation of GIS consists of energy spectra validation, spatial resolution and sensitivity for low and medium energy isotopes. We show that GIS reaches acceleration factors between 5 and 13 over analog GATE simulations for the isotopes in the study. It is a general acceleration technique that can be used for any isotope, phantom and detector combination. Although GIS is useful as a safe and accurate acceleration technique, it cannot deliver clinically acceptable simulation times. The main reason lies in its inability to force photons in a specific direction. In the third part of this dissertation we solve this problem for 99mTc SPECT simulations. Our approach is twofold. Firstly, we introduce two variance reduction techniques: forced detection (FD) and convolution-based forced detection (CFD) with multiple projection sampling (MPS). FD and CFD force copies of photons at decay and at every interaction point to be transported through the phantom in a direction sampled within a solid angle toward the SPECT detector head at all SPECT angles simultaneously. We describe how a weight must be assigned to each photon in order to compensate for the forced direction and non-absorption at emission and scatter. We show how the weights are calculated from the total and differential Compton and Rayleigh cross sections per electron with incorporation of Hubbell’s atomic form factor. In the case of FD all detector interactions are modeled by Monte Carlo, while in the case of CFD the detector is modeled analytically. Secondly, we describe the design of an FD and CFD specialized navigator to accelerate the slow tracking algorithms in GEANT4. The validation study shows that both FD and CFD closely match the analog GATE simulations and that we can obtain an acceleration factor between 3 (FD) and 6 (CFD) orders of magnitude over analog simulations. This allows for the simulation of a realistic acquisition with a torso phantom within 130 seconds. In the fourth part of this dissertation we exploit the intrinsic parallel nature of Monte Carlo simulations. We show how Monte Carlo simulations should scale linearly as a function of the number of processing nodes but that this is usually not achieved due to job setup time, output handling and cluster overhead. We describe how our approach is based on two steps: job distribution and output data handling. The job distribution is based on a time-domain partitioning scheme that retains all experimental parameters and that guarantees the statistical independence of each subsimulation. We also reduce the job setup time by the introduction of a parameterized collimator model for SPECT simulations. We reduce the data output handling time by a chain-based output merger. The scalability study is based on a set of simulations on a 70 CPU cluster and shows an acceleration factor of approximately 66 on 70 CPUs for both PET and SPECT.We also show that our method of parallelization does not introduce any approximations and that it can be readily combined with any of the previous acceleration techniques described above

Planck pre-launch status: The HFI instrument, from specification to actual performance

Context. The High Frequency Instrument (HFI) is one of the two focal instruments of the Planck mission. It will observe the whole sky in six bands in the 100 GHz−1 THz range. Aims. The HFI instrument is designed to measure the cosmic microwave background (CMB) with a sensitivity limited only by fundamental sources: the photon noise of the CMB itself and the residuals left after the removal of foregrounds. The two high frequency bands will provide full maps of the submillimetre sky, featuring mainly extended and point source foregrounds. Systematic effects must be kept at negligible levels or accurately monitored so that the signal can be corrected. This paper describes the HFI design and its characteristics deduced from ground tests and calibration. Methods. The HFI instrumental concept and architecture are feasible only by pushing new techniques to their extreme capabilities, mainly: (i) bolometers working at 100 mK and absorbing the radiation in grids; (ii) a dilution cooler providing 100 mK in microgravity conditions; (iii) a new type of AC biased readout electronics and (iv) optical channels using devices inspired from radio and infrared techniques. Results. The Planck-HFI instrument performance exceeds requirements for sensitivity and control of systematic effects. During ground-based calibration and tests, it was measured at instrument and system levels to be close to or better than the goal specification