Multilevel Optimization for Registration of Deformable Point Clouds.

Handling deformation is one of the biggest challenges associated with point cloud registration. When deformation happens due to the motion of an animated object which actively changes its location and general shape, registration of two instances of the same object turns out to be a challenging task. The focus of this work is to address the problem by leveraging the complementary attributes of local and global geometric structures of the point clouds. We define an energy function which consists of local and global terms, as well as a semi-local term to model the intermediate level geometry of the point cloud. The local energy estimates the transformation parameters at the lowest level by assuming a reduced deformation model. The parameters are estimated in a closed form solution, which are then used to assign the initial probability of a stochastic model working at the intermediate level. The global energy term estimates the overall transformation parameters by minimizing a nonlinear least square function via Gauss-Newton optimization framework. The total energy is optimized in a block coordinate descent fashion, updating one term at a time while keeping others constant. Experiments on three publicly available datasets show that the method performs significantly better than several state-of-the-art algorithms in registering pairwise point cloud data.

Skeletonization of Plant Point Cloud Data Using Stochastic Optimization Framework.

Skeleton extraction from 3D plant point cloud data is an essential prior for myriads of phenotyping studies. Although skeleton extraction from 3D shapes have been studied extensively in the computer vision and graphics literature, handling the case of plants is still an open problem. Drawbacks of the existing approaches include the zigzag structure of the skeleton, nonuniform density of skeleton points, lack of points in the areas having complex geometry structure, and most importantly the lack of biological relevance. With the aim to improve existing skeleton structures of state-of-the-art, we propose a stochastic framework which is supported by the biological structure of the original plant (we consider plants without any leaves). Initially we estimate the branching structure of the plant by the notion of ß-splines to form a curve tree defined as a finite set of curves joined in a tree topology with certain level of smoothness. In the next phase, we force the discrete points in the curve tree to move toward the original point cloud by treating each point in the curve tree as a center of Gaussian, and points in the input cloud data as observations from the Gaussians. The task is to find the correct locations of the Gaussian centroids by maximizing a likelihood. The optimization technique is iterative and is based on the Expectation Maximization (EM) algorithm. The E-step estimates which Gaussian the observed point cloud was sampled from, and the M-step maximizes the negative log-likelihood that the observed points were sampled from the Gaussian Mixture Model (GMM) with respect to the model parameters. We experiment with several real world and synthetic datasets and demonstrate the robustness of the approach over the state-of-the-art.

Plant Species Identification from Occluded Leaf Images.

We present an approach to identify the plant species from the contour information from occluded leaf image using a database of full plant leaves. Although contour based 2D shape matching has been studied extensively in the last couple of decades, matching occluded leaves with full leaf databases is an open and little worked on problem. Classifying occluded plant leaves is even more challenging than full leaf matching because of large variations and complexity of leaf structures. Matching an occluded contour with all the full contours in a database is an NP-hard problem, so our algorithm is necessarily suboptimal. First, we represent the 2D contour points as a ß-Spline curve. Then, we extract interest points on these curves via the Discrete Contour Evolution (DCE) algorithm. We use subgraph matching using the DCE points as graph nodes, which produces a number of open curves for each closed leaf contour. Next, we compute the similarity transformation parameters (translation, rotation, and uniform scaling) for each open curve. We then "overlay" each open curve with the inverse similarity transformed occluded curve and use the Fréchet distance metric to measure the quality of the match, retaining the best η matched curves. Since the Fréchet metric is cheap to compute but not perfectly correlated with the quality of the match, we formulate an energy functional that is well correlated with the quality of the match, but is considerably more expensive to compute. The functional uses local and global curvature, Shape Context descriptors, and String Cut features. We minimize this energy functional using a convex-concave relaxation framework. The curve among these best η curves, that has the minimum energy, is considered to be the best overall match with the occluded leaf. Experiments on three publicly available leaf image database shows that our method is both effective and efficient, outperforming other current state-of-the-art methods. Occlusion is measured as the percentage of the overall contour (and not leaf area) that is missing. We show that our algorithm can, even for leaves with a high amounts of occlusion (say 50 percent occlusion), still identify the best full leaf match from the databases.

Machine Vision System for 3D Plant Phenotyping.

Machine vision for plant phenotyping is an emerging research area for producing high throughput in agriculture and crop science applications. Since 2D based approaches have their inherent limitations, 3D plant analysis is becoming state of the art for current phenotyping technologies. We present an automated system for analyzing plant growth in indoor conditions. A gantry robot system is used to perform scanning tasks in an automated manner throughout the lifetime of the plant. A 3D laser scanner mounted as the robot's payload captures the surface point cloud data of the plant from multiple views. The plant is monitored from the vegetative to reproductive stages in light/dark cycles inside a controllable growth chamber. An efficient 3D reconstruction algorithm is used, by which multiple scans are aligned together to obtain a 3D mesh of the plant, followed by surface area and volume computations. The whole system, including the programmable growth chamber, robot, scanner, data transfer, and analysis is fully automated in such a way that a naive user can, in theory, start the system with a mouse click and get back the growth analysis results at the end of the lifetime of the plant with no intermediate intervention. As evidence of its functionality, we show and analyze quantitative results of the rhythmic growth patterns of the dicot Arabidopsis thaliana (L.), and the monocot barley (Hordeum vulgare L.) plants under their diurnal light/dark cycles.