SlicerAstro: a 3-D interactive visual analytics tool for HI data

SKA precursors are capable of detecting hundreds of galaxies in HI in a single 12 hours pointing. In deeper surveys one will probe more easily faint HI structures, typically located in the vicinity of galaxies, such as tails, filaments, and extraplanar gas. The importance of interactive visualization has proven to be fundamental for the exploration of such data as it helps users to receive immediate feedback when manipulating the data. We have developed SlicerAstro, a 3-D interactive viewer with new analysis capabilities, based on traditional 2-D input/output hardware. These capabilities enhance the data inspection, allowing faster analysis of complex sources than with traditional tools. SlicerAstro is an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing. We demonstrate the capabilities of the current stable binary release of SlicerAstro, which offers the following features: i) handling of FITS files and astronomical coordinate systems; ii) coupled 2-D/3-D visualization; iii) interactive filtering; iv) interactive 3-D masking; v) and interactive 3-D modeling. In addition, SlicerAstro has been designed with a strong, stable and modular C++ core, and its classes are also accessible via Python scripting, allowing great flexibility for user-customized visualization and analysis tasks.Comment: 18 pages, 11 figures, Accepted by Astronomy and Computing. SlicerAstro link: https://github.com/Punzo/SlicerAstro/wiki#get-slicerastr

3-D interactive visualisation tools for HI spectral line imaging

Upcoming HI surveys will deliver such large datasets that automated processing using the full 3-D information to find and characterize HI objects is unavoidable. Full 3-D visualization is an essential tool for enabling qualitative and quantitative inspection and analysis of the 3-D data, which is often complex in nature. Here we present $\tt{SlicerAstro}$, an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing, which we developed for the inspection and analysis of HI spectral line data. We describe its initial capabilities, including 3-D filtering, 3-D selection and comparative modelling

Using treemaps for variable selection in spatio-temporal visualisation

We demonstrate and reflect upon the use of enhanced treemaps that incorporate spatial and temporal ordering for exploring a large multivariate spatio-temporal data set. The resulting data-dense views summarise and simultaneously present hundreds of space-, time-, and variable-constrained subsets of a large multivariate data set in a structure that facilitates their meaningful comparison and supports visual analysis. Interactive techniques allow localised patterns to be explored and subsets of interest selected and compared with the spatial aggregate. Spatial variation is considered through interactive raster maps and high-resolution local road maps. The techniques are developed in the context of 42.2 million records of vehicular activity in a 98 km(2) area of central London and informally evaluated through a design used in the exploratory visualisation of this data set. The main advantages of our technique are the means to simultaneously display hundreds of summaries of the data and to interactively browse hundreds of variable combinations with ordering and symbolism that are consistent and appropriate for space- and time- based variables. These capabilities are difficult to achieve in the case of spatio-temporal data with categorical attributes using existing geovisualisation methods. We acknowledge limitations in the treemap representation but enhance the cognitive plausibility of this popular layout through our two-dimensional ordering algorithm and interactions. Patterns that are expected (e.g. more traffic in central London), interesting (e.g. the spatial and temporal distribution of particular vehicle types) and anomalous (e.g. low speeds on particular road sections) are detected at various scales and locations using the approach. In many cases, anomalies identify biases that may have implications for future use of the data set for analyses and applications. Ordered treemaps appear to have potential as interactive interfaces for variable selection in spatio-temporal visualisation. Information Visualization (2008) 7, 210-224. doi: 10.1057/palgrave.ivs.950018

DoctorEye: A clinically driven multifunctional platform, for accurate processing of tumors in medical images

Copyright @ Skounakis et al.This paper presents a novel, open access interactive platform for 3D medical image analysis, simulation and visualization, focusing in oncology images. The platform was developed through constant interaction and feedback from expert clinicians integrating a thorough analysis of their requirements while having an ultimate goal of assisting in accurately delineating tumors. It allows clinicians not only to work with a large number of 3D tomographic datasets but also to efficiently annotate multiple regions of interest in the same session. Manual and semi-automatic segmentation techniques combined with integrated correction tools assist in the quick and refined delineation of tumors while different users can add different components related to oncology such as tumor growth and simulation algorithms for improving therapy planning. The platform has been tested by different users and over large number of heterogeneous tomographic datasets to ensure stability, usability, extensibility and robustness with promising results. AVAILABILITY: THE PLATFORM, A MANUAL AND TUTORIAL VIDEOS ARE AVAILABLE AT: http://biomodeling.ics.forth.gr. It is free to use under the GNU General Public License

Finding faint HI structure in and around galaxies: scraping the barrel

Soon to be operational HI survey instruments such as APERTIF and ASKAP will produce large datasets. These surveys will provide information about the HI in and around hundreds of galaxies with a typical signal-to-noise ratio of $\sim$ 10 in the inner regions and $\sim$ 1 in the outer regions. In addition, such surveys will make it possible to probe faint HI structures, typically located in the vicinity of galaxies, such as extra-planar-gas, tails and filaments. These structures are crucial for understanding galaxy evolution, particularly when they are studied in relation to the local environment. Our aim is to find optimized kernels for the discovery of faint and morphologically complex HI structures. Therefore, using HI data from a variety of galaxies, we explore state-of-the-art filtering algorithms. We show that the intensity-driven gradient filter, due to its adaptive characteristics, is the optimal choice. In fact, this filter requires only minimal tuning of the input parameters to enhance the signal-to-noise ratio of faint components. In addition, it does not degrade the resolution of the high signal-to-noise component of a source. The filtering process must be fast and be embedded in an interactive visualization tool in order to support fast inspection of a large number of sources. To achieve such interactive exploration, we implemented a multi-core CPU (OpenMP) and a GPU (OpenGL) version of this filter in a 3D visualization environment ($\tt{SlicerAstro}$).Comment: 17 pages, 9 figures, 4 tables. Astronomy and Computing, accepte

Multi-touch 3D Exploratory Analysis of Ocean Flow Models

Modern ocean flow simulations are generating increasingly complex, multi-layer 3D ocean flow models. However, most researchers are still using traditional 2D visualizations to visualize these models one slice at a time. Properly designed 3D visualization tools can be highly effective for revealing the complex, dynamic flow patterns and structures present in these models. However, the transition from visualizing ocean flow patterns in 2D to 3D presents many challenges, including occlusion and depth ambiguity. Further complications arise from the interaction methods required to navigate, explore, and interact with these 3D datasets. We present a system that employs a combination of stereoscopic rendering, to best reveal and illustrate 3D structures and patterns, and multi-touch interaction, to allow for natural and efficient navigation and manipulation within the 3D environment. Exploratory visual analysis is facilitated through the use of a highly-interactive toolset which leverages a smart particle system. Multi-touch gestures allow users to quickly position dye emitting tools within the 3D model. Finally, we illustrate the potential applications of our system through examples of real world significance