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

Styles of underplating in the Marin Headlands Terrane, Franciscan Complex, California

This is a pre-copy-editing, author-produced PDF of an article accepted for publication in The Geological Society of America Special Papers following peer review. The definitive publisher-authenticated version: "Regalla, C., Rowe, C., Harrichhausen, N., Tarling, M. and Singh, J., 2018. Styles of underplating in the Marin Headlands Terrane, Franciscan Complex, California. GSA Special Publications no. 534" is available online at: http://rock.geosociety.org/Store/detail.aspx?id=spe534.Geophysical images and structural cross-sections of accretionary wedges are usually aligned orthogonal to the subduction trench axis. These sections often reveal underplated duplexes of subducted oceanic sediment and igneous crust that record trench-normal shortening and wedge thickening facilitated by down-stepping of the décollement. However, this approach may under-recognize trench-parallel strain and the effects of faulting associated with flexure of the downgoing plate. New mapping of a recently exposed transect across a portion of the Marin Headlands terrane, California, USA documents evidence for structural complexity over short spatio-temporal scales within an underplated system. We document the geometry, kinematics, vergence and internal architecture of faults and folds along ~2.5 km of section, and identify six previously unmapped intra-formational imbricate thrusts and thirteen high-angle faults that accommodate shortening and flattening of the underthrust section. Thrust faults occur within nearly every lithology without clear preference for any stratigraphic horizon, and fold vergence varies between imbricate sheets by ~10-40°. In our map area, imbricate bounding thrusts have relatively narrow damage zones (≤5-10 m), sharp, discrete fault cores, and lack veining, in contrast to the wide, highly-veined fault zones previously documented in the Marin Headlands terrane. The spacing of imbricate thrusts combined with paleo-convergence rates indicates relatively rapid generation of new fault surfaces on ~10-100 ka timescales, a process which may contribute to strain hardening and locking within the seismogenic zone. The structural and kinematic complexity documented in the Marin Headlands are an example of the short spatial and temporal scales of heterogeneity that may characterize regions of active underplating. Such features are smaller than the typical spatial resolution of geophysical data from active subduction thrusts, and may not be readily resolved, thus highlighting the need for cross-comparison of geophysical data with field analogues when evaluating the kinematic and mechanical processes of underplating

Focus+Context via Snaking Paths

Focus+context visualizations reveal specific structures in high detail while effectively depicting its surroundings, often relying on transitions between the two areas to provide context. We present an approach to generate focus+context visualizations depicting cylindrical structures along snaking paths that enables the structures themselves to become the transitions and focal areas, simultaneously. A method to automatically create a snaking path through space by applying a path finding algorithm is presented. A 3D curve is created based on the 2D snaking path. We describe a process to deform cylindrical structures in segmented volumetric models to match the curve and provide preliminary geometric models as templates for artists to build upon. Structures are discovered using our constrained volumetric sculpting method that enables removal of occluding material while leaving them intact. We find the resulting visualizations effectively mimic a set of motivating illustrations and discuss some limitations of the automatic approach

Real-Time RGB-D based Template Matching Pedestrian Detection

Pedestrian detection is one of the most popular topics in computer vision and robotics. Considering challenging issues in multiple pedestrian detection, we present a real-time depth-based template matching people detector. In this paper, we propose different approaches for training the depth-based template. We train multiple templates for handling issues due to various upper-body orientations of the pedestrians and different levels of detail in depth-map of the pedestrians with various distances from the camera. And, we take into account the degree of reliability for different regions of sliding window by proposing the weighted template approach. Furthermore, we combine the depth-detector with an appearance based detector as a verifier to take advantage of the appearance cues for dealing with the limitations of depth data. We evaluate our method on the challenging ETH dataset sequence. We show that our method outperforms the state-of-the-art approaches.Comment: published in ICRA 201

Video Object Detection with an Aligned Spatial-Temporal Memory

We introduce Spatial-Temporal Memory Networks for video object detection. At its core, a novel Spatial-Temporal Memory module (STMM) serves as the recurrent computation unit to model long-term temporal appearance and motion dynamics. The STMM's design enables full integration of pretrained backbone CNN weights, which we find to be critical for accurate detection. Furthermore, in order to tackle object motion in videos, we propose a novel MatchTrans module to align the spatial-temporal memory from frame to frame. Our method produces state-of-the-art results on the benchmark ImageNet VID dataset, and our ablative studies clearly demonstrate the contribution of our different design choices. We release our code and models at http://fanyix.cs.ucdavis.edu/project/stmn/project.html

Relating cell shape and mechanical stress in a spatially disordered epithelium using a vertex-based model

Using a popular vertex-based model to describe a spatially disordered planar epithelial monolayer, we examine the relationship between cell shape and mechanical stress at the cell and tissue level. Deriving expressions for stress tensors starting from an energetic formulation of the model, we show that the principal axes of stress for an individual cell align with the principal axes of shape, and we determine the bulk effective tissue pressure when the monolayer is isotropic at the tissue level. Using simulations for a monolayer that is not under peripheral stress, we fit parameters of the model to experimental data for Xenopus embryonic tissue. The model predicts that mechanical interactions can generate mesoscopic patterns within the monolayer that exhibit long-range correlations in cell shape. The model also suggests that the orientation of mechanical and geometric cues for processes such as cell division are likely to be strongly correlated in real epithelia. Some limitations of the model in capturing geometric features of Xenopus epithelial cells are highlighted.Comment: 29 pages, 10 figures, revisio