Calibration Challenges for Future Radio Telescopes

Instruments for radio astronomical observations have come a long way. While the first telescopes were based on very large dishes and 2-antenna interferometers, current instruments consist of dozens of steerable dishes, whereas future instruments will be even larger distributed sensor arrays with a hierarchy of phased array elements. For such arrays to provide meaningful output (images), accurate calibration is of critical importance. Calibration must solve for the unknown antenna gains and phases, as well as the unknown atmospheric and ionospheric disturbances. Future telescopes will have a large number of elements and a large field of view. In this case the parameters are strongly direction dependent, resulting in a large number of unknown parameters even if appropriately constrained physical or phenomenological descriptions are used. This makes calibration a daunting parameter estimation task, that is reviewed from a signal processing perspective in this article.Comment: 12 pages, 7 figures, 20 subfigures The title quoted in the meta-data is the title after release / final editing

MEG and EEG data analysis with MNE-Python

Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals generated by neuronal activity in the brain. Using these signals to characterize and locate neural activation in the brain is a challenge that requires expertise in physics, signal processing, statistics, and numerical methods. As part of the MNE software suite, MNE-Python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in Python that cover multiple methods of data preprocessing, source localization, statistical analysis, and estimation of functional connectivity between distributed brain regions. All algorithms and utility functions are implemented in a consistent manner with well-documented interfaces, enabling users to create M/EEG data analysis pipelines by writing Python scripts. Moreover, MNE-Python is tightly integrated with the core Python libraries for scientific comptutation (NumPy, SciPy) and visualization (matplotlib and Mayavi), as well as the greater neuroimaging ecosystem in Python via the Nibabel package. The code is provided under the new BSD license allowing code reuse, even in commercial products. Although MNE-Python has only been under heavy development for a couple of years, it has rapidly evolved with expanded analysis capabilities and pedagogical tutorials because multiple labs have collaborated during code development to help share best practices. MNE-Python also gives easy access to preprocessed datasets, helping users to get started quickly and facilitating reproducibility of methods by other researchers. Full documentation, including dozens of examples, is available at http://martinos.org/mne

Localising epileptiform activity and eloquent cortex using magnetoencephalography

In patients with drug resistant epilepsy, the surgical resection of epileptogenic cortex allows the possibility for seizure freedom, provided that epileptogenic and eloquent brain tissue can be accurately identified prior to surgery. This is often achieved using various techniques including neuroimaging, electroencephalographic (EEG), neuropsychological and invasive measurements. Over the last 20 years, magnetoencephalography (MEG) has emerged as a non-invasive tool that can provide important clinical information to patients with suspected neocortical epilepsy being considered for surgery. The standard clinical MEG analyses to localise abnormalities are not always successful and therefore the development and evaluation of alternative methods are warranted. There is also a continuous need to develop MEG techniques to delineate eloquent cortex. Based on this rationale, this thesis is concerned with the presurgical evaluation of drug resistant epilepsy patients using MEG and consists of two themes: the first theme focuses on the refinement of techniques to functionally map the brain and the second focuses on evaluating alternative techniques to localise epileptiform activity. The first theme involved the development of an alternative beamformer pipeline to analyse Elekta Neuromag data and was subsequently applied to data acquired using a pre-existing and a novel language task. The findings of the second theme demonstrated how beamformer based measures can objectively localise epileptiform abnormalities. A novel measure, rank vector entropy, was introduced to facilitate the detection of multiple types of abnormal signals (e.g. spikes, slow waves, low amplitude transients). This thesis demonstrates the clinical capacity of MEG and its role in the presurgical evaluation of drug resistant epilepsy patients

Estimating neural currents from neuromagnetic measurements

This thesis concerns three new methods for estimating the electrical activity of the human brain from the magnetic fields measured outside the head. The first method models the electrical activity as a combination of focal current dipoles and applies global optimization to estimate their locations without need for an initial solution. The second method is the minimum current estimate that is capable of modeling both focal and distributed electrical activity. The third method measures the movements of the head during the measurements and uses this information for more accurate estimates of the neural currents. The usability of the methods is demonstrated using simulations and measurements. The minimum current estimate is also applied to four experiments of cognitive processes in the human brain: one studying visuomotor interaction, second studying visual attention, third studying integration of auditory and visual representations of letters, and fourth studying observation of sign language in signing and non-signing subjects.reviewe

EXPLORING NANOSCALE SPIN PHYSICS USING SINGLE SPINS IN DIAMOND

Understanding spin physics and controlling solid-state spins at nanometer length scales is of crucial importance in modern physics research. Because of the atomic-scale dimensions, long coherence time, and optical readout, Nitrogen-Vacancy centers (NV centers) in diamond have become prominent for exploring topics in nanoscale spin physics. In this thesis, two questions are investigated using single NV centers: what mechanisms limit the control and measurement of geometric phase of a single solid-state spin qubit, and whether it is feasible to detect electron spin resonance in submicron volumes from copper-ion-labeled molecules. We have obtained limits on the fidelity of geometric phase gates, and showed using newly developed quantum sensing techniques that we are indeed able to detect such extremely weak signals, down to the single spin limit. Our results with NV centers in measuring single electron spins opens the door to a variety of applications of NV center magnetometry in interdisciplinary topics such as research on the dynamics of protein molecules with copper ion labels

Single atom imaging with time-resolved electron microscopy

Developments in scanning transmission electron microscopy (STEM) have opened up new possibilities for time-resolved imaging at the atomic scale. However, rapid imaging of single atom dynamics brings with it a new set of challenges, particularly regarding noise and the interaction between the electron beam and the specimen. This thesis develops a set of analytical tools for capturing atomic motion and analyzing the dynamic behaviour of materials at the atomic scale. Machine learning is increasingly playing an important role in the analysis of electron microscopy data. In this light, new unsupervised learning tools are developed here for noise removal under low-dose imaging conditions and for identifying the motion of surface atoms. The scope for real-time processing and analysis is also explored, which is of rising importance as electron microscopy datasets grow in size and complexity. These advances in image processing and analysis are combined with computational modelling to uncover new chemical and physical insights into the motion of atoms adsorbed onto surfaces. Of particular interest are systems for heterogeneous catalysis, where the catalytic activity can depend intimately on the atomic environment. The study of Cu atoms on a graphene oxide support reveals that the atoms undergo anomalous diffusion as a result of spatial and energetic disorder present in the substrate. The investigation is extended to examine the structure and stability of small Cu clusters on graphene oxide, with atomistic modelling used to understand the significant role played by the substrate. Finally, the analytical methods are used to study the surface reconstruction of silicon alongside the electron beam-induced motion of adatoms on the surface. Taken together, these studies demonstrate the materials insights that can be obtained with time-resolved STEM imaging, and highlight the importance of combining state-ofthe- art imaging with computational analysis and atomistic modelling to quantitatively characterize the behaviour of materials with atomic resolution.The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007–2013)/ERC grant agreement 291522–3DIMAGE, as well as from the European Union Seventh Framework Programme under Grant Agreement 312483-ESTEEM2 (Integrated Infrastructure Initiative -I3)

Efficient Human Activity Recognition in Large Image and Video Databases

Vision-based human action recognition has attracted considerable interest in recent research for its applications to video surveillance, content-based search, healthcare, and interactive games. Most existing research deals with building informative feature descriptors, designing efficient and robust algorithms, proposing versatile and challenging datasets, and fusing multiple modalities. Often, these approaches build on certain conventions such as the use of motion cues to determine video descriptors, application of off-the-shelf classifiers, and single-factor classification of videos. In this thesis, we deal with important but overlooked issues such as efficiency, simplicity, and scalability of human activity recognition in different application scenarios: controlled video environment (e.g.~indoor surveillance), unconstrained videos (e.g.~YouTube), depth or skeletal data (e.g.~captured by Kinect), and person images (e.g.~Flicker). In particular, we are interested in answering questions like (a) is it possible to efficiently recognize human actions in controlled videos without temporal cues? (b) given that the large-scale unconstrained video data are often of high dimension low sample size (HDLSS) nature, how to efficiently recognize human actions in such data? (c) considering the rich 3D motion information available from depth or motion capture sensors, is it possible to recognize both the actions and the actors using only the motion dynamics of underlying activities? and (d) can motion information from monocular videos be used for automatically determining saliency regions for recognizing actions in still images