3D Scanning System for Automatic High-Resolution Plant Phenotyping

Thin leaves, fine stems, self-occlusion, non-rigid and slowly changing structures make plants difficult for three-dimensional (3D) scanning and reconstruction -- two critical steps in automated visual phenotyping. Many current solutions such as laser scanning, structured light, and multiview stereo can struggle to acquire usable 3D models because of limitations in scanning resolution and calibration accuracy. In response, we have developed a fast, low-cost, 3D scanning platform to image plants on a rotating stage with two tilting DSLR cameras centred on the plant. This uses new methods of camera calibration and background removal to achieve high-accuracy 3D reconstruction. We assessed the system's accuracy using a 3D visual hull reconstruction algorithm applied on 2 plastic models of dicotyledonous plants, 2 sorghum plants and 2 wheat plants across different sets of tilt angles. Scan times ranged from 3 minutes (to capture 72 images using 2 tilt angles), to 30 minutes (to capture 360 images using 10 tilt angles). The leaf lengths, widths, areas and perimeters of the plastic models were measured manually and compared to measurements from the scanning system: results were within 3-4% of each other. The 3D reconstructions obtained with the scanning system show excellent geometric agreement with all six plant specimens, even plants with thin leaves and fine stems.Comment: 8 papes, DICTA 201

Saliency detection for large-scale mesh decimation

Highly complex and dense models of 3D objects have recently become indispensable in digital industries. Mesh decimation then plays a crucial role in the production pipeline to efficiently get visually convincing yet compact expressions of complex meshes. However, the current pipeline typically does not allow artists control the decimation process, just a simplification rate. Thus a preferred approach in production settings splits the process into a first pass of saliency detection highlighting areas of greater detail, and allowing artists to iterate until satisfied before simplifying the model. We propose a novel, efficient multi-scale method to compute mesh saliency at coarse and finer scales, based on fast mesh entropy of local surface measurements. Unlike previous approaches, we ensure a robust and straightforward calculation of mesh saliency even for densely tessellated models with millions of polygons. Moreover, we introduce a new adaptive subsampling and interpolation algorithm for saliency estimation. Our implementation achieves speedups of up to three orders of magnitude over prior approaches. Experimental results showcase its resilience to problem scenarios that efficiently scales up to process multi-million vertex meshes. Our evaluation with artists in the entertainment industry also demonstrates its applicability to real use-case scenarios

Region-wide temporal and spatial variation in Caribbean reef architecture: is coral cover the whole story?

The architectural complexity of coral reefs is largely generated by reef-building corals, yet the effects of current regional-scale declines in coral cover on reef complexity are poorly understood. In particular, both the extent to which declines in coral cover lead to declines in complexity and the length of time it takes for reefs to collapse following coral mortality are unknown. Here we assess the extent of temporal and spatial covariation between coral cover and reef architectural complexity using a Caribbean-wide dataset of temporally replicated estimates spanning four decades. Both coral cover and architectural complexity have declined rapidly over time, with little evidence of a time-lag. However, annual rates of change in coral cover and complexity do not covary, and levels of complexity vary greatly among reefs with similar coral cover. These findings suggest that the stressors influencing Caribbean reefs are sufficiently severe and widespread to produce similar regional-scale declines in coral cover and reef complexity, even though reef architectural complexity is not a direct function of coral cover at local scales. Given that architectural complexity is not a simple function of coral cover, it is important that conservation monitoring and restoration give due consideration to both architecture and coral cover. This will help ensure that the ecosystem services supported by architectural complexity, such as nutrient recycling, dissipation of wave energy, fish production and diversity, are maintained and enhanced

ProSAS: a database for analyzing alternative splicing in the context of protein structures

Alternative splicing is known to be one of the major sources for functional diversity in higher eukaryotes. Several splicing isoforms have been characterized in the literature that play important roles in cellular processes like apoptosis or signal transduction pathways. Splicing events can often be detected on the mRNA level by large-scale cDNA or EST experiments and such data is collected and annotated in several databases. Nevertheless, the effects of splicing on the structure of a protein are largely unknown. The ProSAS (Protein Structure and Alternative Splicing) database fills this gap and provides a unified resource for analyzing effects of alternative splicing events in the context of protein structures. ProSAS comprehensively annotates and models protein structures for several Ensembl genomes as well as SwissProt entries harbouring splicing events. Alternative isoforms annotated in Ensembl or SwissProt can be analyzed on the protein structure and protein function level using an intuitive user interface that provides several features and tools for a structure-based analysis of alternative splicing events. The ProSAS database is freely accessible at http://www.bio.ifi.lmu.de/ProSAS

A Synthetic-Vision Based Steering Approach for Crowd Simulation

International audienceIn the everyday exercise of controlling their locomotion, humans rely on their optic flow of the perceived environment to achieve collision-free navigation. In crowds, in spite of the complexity of the environment made of numerous obstacles, humans demonstrate remarkable capacities in avoiding collisions. Cognitive science work on human locomotion states that relatively succinct information is extracted from the optic flow to achieve safe locomotion. In this paper, we explore a novel vision-based approach of collision avoidance between walkers that fits the requirements of interactive crowd simulation. By simulating humans based on cognitive science results, we detect future collisions as well as the level of danger from visual stimuli. The motor-response is twofold: a reorientation strategy prevents future collision, whereas a deceleration strategy prevents imminent collisions. Several examples of our simulation results show that the emergence of self-organized patterns of walkers is reinforced using our approach. The emergent phenomena are visually appealing. More importantly, they improve the overall efficiency of the walkers' traffic and avoid improbable locking situations

Metameric Inpainting for Image Warping

Image-warping , a per-pixel deformation of one image into another, is an essential component in immersive visual experiences such as virtual reality or augmented reality. The primary issue with image warping is disocclusions, where occluded (and hence unknown) parts of the input image would be required to compose the output image. We introduce a new image warping method, Metameric image inpainting - an approach for hole-filling in real-time with foundations in human visual perception. Our method estimates image feature statistics of disoccluded regions from their neighbours. These statistics are inpainted and used to synthesise visuals in real-time that are less noticeable to study participants, particularly in peripheral vision. Our method offers speed improvements over the standard structured image inpainting methods while improving realism over colour-based inpainting such as push-pull. Hence, our work paves the way towards future applications such as depth image-based rendering, 6-DoF 360 rendering, and remote render-streaming

TGF-b Superfamily Cytokine MIC-1/GDF15 Is a Physiological Appetite and Body Weight Regulator

The TGF-b superfamily cytokine MIC-1/GDF15 circulates in all humans and when overproduced in cancer leads to anorexia/cachexia, by direct action on brain feeding centres. In these studies we have examined the role of physiologically relevant levels of MIC-1/GDF15 in the regulation of appetite, body weight and basal metabolic rate. MIC-1/GDF15 gene knockout mice (MIC-1−/−) weighed more and had increased adiposity, which was associated with increased spontaneous food intake. Female MIC-1−/− mice exhibited some additional alterations in reduced basal energy expenditure and physical activity, possibly owing to the associated decrease in total lean mass. Further, infusion of human recombinant MIC-1/GDF15 sufficient to raise serum levels in MIC-1−/− mice to within the normal human range reduced body weight and food intake. Taken together, our findings suggest that MIC-1/GDF15 is involved in the physiological regulation of appetite and energy storage

Half-Dead Colonies of Montastraea Annularis Release Viable Gametes On A Degraded Reef In The Us Virgin Islands

This article contributes to scholarship on Afroeurope by investigating the intersection of blackness, Africanness, and Europeanness in everyday discourses and social practices in the Netherlands and Italy. We examine how young African-descended Europeans are forging new ways of being both African and European through practices of self-making, which should be understood against both the historical background of colonialism and the contemporary politics of othering. Such practices take on an urgency for these youth, often encompassing a reinvention of Africanness and/or blackness as well as a challenge to dominant, exclusionary understandings of Europeanness. Comparing Afro-Dutch and Afro-Italian modes of self-making, centred on African heritage and roots, we discuss: 1) the emergence of a transnational, Afroeuropean imaginary, distinguished from both white Europe and African-American formations; and 2) the diversity of Afroeuropean modes of self-making, all rooted in distinct histories of colonialism, slavery, and immigration, and influenced by global formations of Africanness and blackness. These new Afro and African identities advanced by young Europeans do not turn away from Europeanness (as dominant identity models would assume: the more African, the less European), nor simply add to Europeanness (“multicultural” identities), nor even mix with Europeanness (“hybrid” identities), but are in and of themselves European

Effects of ocean acidification on invertebrate settlement at volcanic CO<inf>2</inf> vents

We present the first study of the effects of ocean acidification on settlement of benthic invertebrates and microfauna. Artificial collectors were placed for 1 month along pH gradients at CO2 vents off Ischia (Tyrrhenian Sea, Italy). Seventy-nine taxa were identified from six main taxonomic groups (foraminiferans, nematodes, polychaetes, molluscs, crustaceans and chaetognaths). Calcareous foraminiferans, serpulid polychaetes, gastropods and bivalves showed highly significant reductions in recruitment to the collectors as pCO2 rose from normal (336-341 ppm, pH 8.09-8.15) to high levels (886-5,148 ppm) causing acidified conditions near the vents (pH 7.08-7.79). Only the syllid polychaete Syllis prolifera had higher abundances at the most acidified station, although a wide range of polychaetes and small crustaceans was able to settle and survive under these conditions. A few taxa (Amphiglena mediterranea, Leptochelia dubia, Caprella acanthifera) were particularly abundant at stations acidified by intermediate amounts of CO2 (pH 7. 41-7.99). These results show that increased levels of CO2 can profoundly affect the settlement of a wide range of benthic organisms. © 2010 Springer-Verlag