Single-picture reconstruction and rendering of trees for plausible vegetation synthesis

State-of-the-art approaches for tree reconstruction either put limiting constraints on the input side (requiring multiple photographs, a scanned point cloud or intensive user input) or provide a representation only suitable for front views of the tree. In this paper we present a complete pipeline for synthesizing and rendering detailed trees from a single photograph with minimal user effort. Since the overall shape and appearance of each tree is recovered from a single photograph of the tree crown, artists can benefit from georeferenced images to populate landscapes with native tree species. A key element of our approach is a compact representation of dense tree crowns through a radial distance map. Our first contribution is an automatic algorithm for generating such representations from a single exemplar image of a tree. We create a rough estimate of the crown shape by solving a thin-plate energy minimization problem, and then add detail through a simplified shape-from-shading approach. The use of seamless texture synthesis results in an image-based representation that can be rendered from arbitrary view directions at different levels of detail. Distant trees benefit from an output-sensitive algorithm inspired on relief mapping. For close-up trees we use a billboard cloud where leaflets are distributed inside the crown shape through a space colonization algorithm. In both cases our representation ensures efficient preservation of the crown shape. Major benefits of our approach include: it recovers the overall shape from a single tree image, involves no tree modeling knowledge and minimal authoring effort, and the associated image-based representation is easy to compress and thus suitable for network streaming.Peer ReviewedPostprint (author's final draft

Reconstructing the Forest of Lineage Trees of Diverse Bacterial Communities Using Bio-inspired Image Analysis

Cell segmentation and tracking allow us to extract a plethora of cell attributes from bacterial time-lapse cell movies, thus promoting computational modeling and simulation of biological processes down to the single-cell level. However, to analyze successfully complex cell movies, imaging multiple interacting bacterial clones as they grow and merge to generate overcrowded bacterial communities with thousands of cells in the field of view, segmentation results should be near perfect to warrant good tracking results. We introduce here a fully automated closed-loop bio-inspired computational strategy that exploits prior knowledge about the expected structure of a colony's lineage tree to locate and correct segmentation errors in analyzed movie frames. We show that this correction strategy is effective, resulting in improved cell tracking and consequently trustworthy deep colony lineage trees. Our image analysis approach has the unique capability to keep tracking cells even after clonal subpopulations merge in the movie. This enables the reconstruction of the complete Forest of Lineage Trees (FLT) representation of evolving multi-clonal bacterial communities. Moreover, the percentage of valid cell trajectories extracted from the image analysis almost doubles after segmentation correction. This plethora of trustworthy data extracted from a complex cell movie analysis enables single-cell analytics as a tool for addressing compelling questions for human health, such as understanding the role of single-cell stochasticity in antibiotics resistance without losing site of the inter-cellular interactions and microenvironment effects that may shape it

A Deep and Autoregressive Approach for Topic Modeling of Multimodal Data

Topic modeling based on latent Dirichlet allocation (LDA) has been a framework of choice to deal with multimodal data, such as in image annotation tasks. Another popular approach to model the multimodal data is through deep neural networks, such as the deep Boltzmann machine (DBM). Recently, a new type of topic model called the Document Neural Autoregressive Distribution Estimator (DocNADE) was proposed and demonstrated state-of-the-art performance for text document modeling. In this work, we show how to successfully apply and extend this model to multimodal data, such as simultaneous image classification and annotation. First, we propose SupDocNADE, a supervised extension of DocNADE, that increases the discriminative power of the learned hidden topic features and show how to employ it to learn a joint representation from image visual words, annotation words and class label information. We test our model on the LabelMe and UIUC-Sports data sets and show that it compares favorably to other topic models. Second, we propose a deep extension of our model and provide an efficient way of training the deep model. Experimental results show that our deep model outperforms its shallow version and reaches state-of-the-art performance on the Multimedia Information Retrieval (MIR) Flickr data set.Comment: 24 pages, 10 figures. A version has been accepted by TPAMI on Aug 4th, 2015. Add footnote about how to train the model in practice in Section 5.1. arXiv admin note: substantial text overlap with arXiv:1305.530

Optimal modeling for complex system design

The article begins with a brief introduction to the theory describing optimal data compression systems and their performance. A brief outline is then given of a representative algorithm that employs these lessons for optimal data compression system design. The implications of rate-distortion theory for practical data compression system design is then described, followed by a description of the tensions between theoretical optimality and system practicality and a discussion of common tools used in current algorithms to resolve these tensions. Next, the generalization of rate-distortion principles to the design of optimal collections of models is presented. The discussion focuses initially on data compression systems, but later widens to describe how rate-distortion theory principles generalize to model design for a wide variety of modeling applications. The article ends with a discussion of the performance benefits to be achieved using the multiple-model design algorithms

NMDA-based pattern discrimination in a modeled cortical neuron

Compartmental simulations of an anatomically characterized cortical pyramidal cell were carried out to study the integrative behavior of a complex dendritic tree. Previous theoretical (Feldman and Ballard 1982; Durbin and Rumelhart 1989; Mel 1990; Mel and Koch 1990; Poggio and Girosi 1990) and compartmental modeling (Koch et al. 1983; Shepherd et al. 1985; Koch and Poggio 1987; Rall and Segev 1987; Shepherd and Brayton 1987; Shepherd et al. 1989; Brown et al. 1991) work had suggested that multiplicative interactions among groups of neighboring synapses could greatly enhance the processing power of a neuron relative to a unit with only a single global firing threshold. This issue was investigated here, with a particular focus on the role of voltage-dependent N-methyl-D-asparate (NMDA) channels in the generation of cell responses. First, it was found that when a large proportion of the excitatory synaptic input to dendritic spines is carried by NMDA channels, the pyramidal cell responds preferentially to spatially clustered, rather than random, distributions of activated synapses. Second, based on this mechanism, the NMDA-rich neuron is shown to be capable of solving a nonlinear pattern discrimination task. We propose that manipulation of the spatial ordering of afferent synaptic connections onto the dendritic arbor is a possible biological strategy for pattern information storage during learning

Interactive Vegetation Rendering with Slicing and Blending

Detailed and interactive 3D rendering of vegetation is one of the challenges of traditional polygon-oriented computer graphics, due to large geometric complexity even of simple plants. In this paper we introduce a simplified image-based rendering approach based solely on alpha-blended textured polygons. The simplification is based on the limitations of human perception of complex geometry. Our approach renders dozens of detailed trees in real-time with off-the-shelf hardware, while providing significantly improved image quality over existing real-time techniques. The method is based on using ordinary mesh-based rendering for the solid parts of a tree, its trunk and limbs. The sparse parts of a tree, its twigs and leaves, are instead represented with a set of slices, an image-based representation. A slice is a planar layer, represented with an ordinary alpha or color-keyed texture; a set of parallel slices is a slicing. Rendering from an arbitrary viewpoint in a 360 degree circle around the center of a tree is achieved by blending between the nearest two slicings. In our implementation, only 6 slicings with 5 slices each are sufficient to visualize a tree for a moving or stationary observer with the perceptually similar quality as the original model