Unwind: Interactive Fish Straightening

The ScanAllFish project is a large-scale effort to scan all the world's 33,100 known species of fishes. It has already generated thousands of volumetric CT scans of fish species which are available on open access platforms such as the Open Science Framework. To achieve a scanning rate required for a project of this magnitude, many specimens are grouped together into a single tube and scanned all at once. The resulting data contain many fish which are often bent and twisted to fit into the scanner. Our system, Unwind, is a novel interactive visualization and processing tool which extracts, unbends, and untwists volumetric images of fish with minimal user interaction. Our approach enables scientists to interactively unwarp these volumes to remove the undesired torque and bending using a piecewise-linear skeleton extracted by averaging isosurfaces of a harmonic function connecting the head and tail of each fish. The result is a volumetric dataset of a individual, straight fish in a canonical pose defined by the marine biologist expert user. We have developed Unwind in collaboration with a team of marine biologists: Our system has been deployed in their labs, and is presently being used for dataset construction, biomechanical analysis, and the generation of figures for scientific publication

Publishing Time Dependent Oceanographic Visualizations using VRML

Oceanographic simulations generate time dependent data; thus, visualizations of this data should include and realize the variable `time'. Moreover, the oceanographers are located across the world and they wish to conveniently communicate and exchange these temporal realizations. This publication of material may be achieved using different methods and languages. VRML provides one convenient publication medium that allows the visualizations to be easily viewed and exchanged between users. Using VRML as the implementation language, we describe five categories of operation. The strategies are determined by the level of calculation that is achieved at the generation stage compared to the playing of the animation. We name the methods: 2D movie, 3D spatial, 3D flipbook, key frame deformation and visualization program

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

Imaging Informatics and the Human Brain Project: the Role of Structure, Review

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Unrest at Domuyo Volcano, Argentina, detected by geophysical and geodetic data and morphometric analysis

New volcanic unrest has been detected in the Domuyo Volcanic Center (DVC), to the east of the Andes Southern Volcanic Zone in Argentina. To better understand this activity, we investigated new seismic monitoring data, gravimetric and magnetic campaign data, and interferometric synthetic aperture radar (InSAR) deformation maps, and we derived an image of the magma plumbing system and the likely source of the unrest episode. Seismic events recorded during 2017-2018 nucleate beneath the southwestern flank of the DVC. Ground deformation maps derived from InSAR processing of Sentinel-1 data exhibit an inflation area exceeding 300 km2, from 2014 to at least March 2018, which can be explained by an inflating sill model located 7 km deep. The Bouguer anomaly reveals a negative density contrast of ~35 km wavelength, which is spatially coincident with the InSAR pattern. Our 3D density modeling suggests a body approximately 4-6 km deep with a density contrast of -550 kg/m3. Therefore, the geophysical and geodetic data allow identification of the plumbing system that is subject to inflation at these shallow crustal depths. We compared the presence and dimensions of the inferred doming area to the drainage patterns of the area, which support long-established incremental uplift according to morphometric analysis. Future studies will allow us to investigate further whether the new unrest is hydrothermal or magmatic in origin.Fil: Astort, Ana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; ArgentinaFil: Walter, Thomas R. German Research Centre for Geosciences; AlemaniaFil: Ruiz, Francisco. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto Geofísico Sismológico Volponi; ArgentinaFil: Sagripanti, Lucía. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; ArgentinaFil: Nacif, Andres Antonio. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto Geofísico Sismológico Volponi; ArgentinaFil: Acosta, Gemma. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto Geofísico Sismológico Volponi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Folguera Telichevsky, Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; Argentin