Computer Vision Problems in 3D Plant Phenotyping

In recent years, there has been significant progress in Computer Vision based plant phenotyping (quantitative analysis of biological properties of plants) technologies. Traditional methods of plant phenotyping are destructive, manual and error prone. Due to non-invasiveness and non-contact properties as well as increased accuracy, imaging techniques are becoming state-of-the-art in plant phenotyping. Among several parameters of plant phenotyping, growth analysis is very important for biological inference. Automating the growth analysis can result in accelerating the throughput in crop production. This thesis contributes to the automation of plant growth analysis. First, we present a novel system for automated and non-invasive/non-contact plant growth measurement. We exploit the recent advancements of sophisticated robotic technologies and near infrared laser scanners to build a 3D imaging system and use state-of-the-art Computer Vision algorithms to fully automate growth measurement. We have set up a gantry robot system having 7 degrees of freedom hanging from the roof of a growth chamber. The payload is a range scanner, which can measure dense depth maps (raw 3D coordinate points in mm) on the surface of an object (the plant). The scanner can be moved around the plant to scan from different viewpoints by programming the robot with a specific trajectory. The sequence of overlapping images can be aligned to obtain a full 3D structure of the plant in raw point cloud format, which can be triangulated to obtain a smooth surface (triangular mesh), enclosing the original plant. We show the capability of the system to capture the well known diurnal pattern of plant growth computed from the surface area and volume of the plant meshes for a number of plant species. Second, we propose a technique to detect branch junctions in plant point cloud data. We demonstrate that using these junctions as feature points, the correspondence estimation can be formulated as a subgraph matching problem, and better matching results than state-of-the-art can be achieved. Also, this idea removes the requirement of a priori knowledge about rotational angles between adjacent scanning viewpoints imposed by the original registration algorithm for complex plant data. Before, this angle information had to be approximately known. Third, we present an algorithm to classify partially occluded leaves by their contours. In general, partial contour matching is a NP-hard problem. We propose a suboptimal matching solution and show that our method outperforms state-of-the-art on 3 public leaf datasets. We anticipate using this algorithm to track growing segmented leaves in our plant range data, even when a leaf becomes partially occluded by other plant matter over time. Finally, we perform some experiments to demonstrate the capability and limitations of the system and highlight the future research directions for Computer Vision based plant phenotyping

Computer Vision Problems in 3D Plant Phenotyping

In recent years, there has been significant progress in Computer Vision based plant phenotyping (quantitative analysis of biological properties of plants) technologies. Traditional methods of plant phenotyping are destructive, manual and error prone. Due to non-invasiveness and non-contact properties as well as increased accuracy, imaging techniques are becoming state-of-the-art in plant phenotyping. Among several parameters of plant phenotyping, growth analysis is very important for biological inference. Automating the growth analysis can result in accelerating the throughput in crop production. This thesis contributes to the automation of plant growth analysis. First, we present a novel system for automated and non-invasive/non-contact plant growth measurement. We exploit the recent advancements of sophisticated robotic technologies and near infrared laser scanners to build a 3D imaging system and use state-of-the-art Computer Vision algorithms to fully automate growth measurement. We have set up a gantry robot system having 7 degrees of freedom hanging from the roof of a growth chamber. The payload is a range scanner, which can measure dense depth maps (raw 3D coordinate points in mm) on the surface of an object (the plant). The scanner can be moved around the plant to scan from different viewpoints by programming the robot with a specific trajectory. The sequence of overlapping images can be aligned to obtain a full 3D structure of the plant in raw point cloud format, which can be triangulated to obtain a smooth surface (triangular mesh), enclosing the original plant. We show the capability of the system to capture the well known diurnal pattern of plant growth computed from the surface area and volume of the plant meshes for a number of plant species. Second, we propose a technique to detect branch junctions in plant point cloud data. We demonstrate that using these junctions as feature points, the correspondence estimation can be formulated as a subgraph matching problem, and better matching results than state-of-the-art can be achieved. Also, this idea removes the requirement of a priori knowledge about rotational angles between adjacent scanning viewpoints imposed by the original registration algorithm for complex plant data. Before, this angle information had to be approximately known. Third, we present an algorithm to classify partially occluded leaves by their contours. In general, partial contour matching is a NP-hard problem. We propose a suboptimal matching solution and show that our method outperforms state-of-the-art on 3 public leaf datasets. We anticipate using this algorithm to track growing segmented leaves in our plant range data, even when a leaf becomes partially occluded by other plant matter over time. Finally, we perform some experiments to demonstrate the capability and limitations of the system and highlight the future research directions for Computer Vision based plant phenotyping

Non-parametric coupled shape priors for segmentation of deformable objects in time-series images using particle filters

Segmentation is usually the first step in image processing and directly impacts the success or failure of the image analysis algorithm. It turns into a very challenging problem when the observed image suffers from insufficiencies, such as high level of noise, clutter, data loss and, occlusion. The effect of prior knowledge has been widely studied in the curve evolution-based models and it has been proved that utilization of some kind of prior information obtained by exploiting the known features of the object to be segmented, can aid the result of the segmentation process. In this thesis, shape, which is a favorable attribute of the object to be segmented, is used to form the prior information. The proposed method has been developed based on a sampling approach using sequential Monte Carlo (Particle Filters) and In order to enrich the segmentation model, a new term is introduced which we refer to as coupled shape priors. By involving a curve evolution step into the sampling process, the coupled shape prior term, takes part in the proposed energy functional defined for the curve evolution step and incorporates the temporal shape dependencies. The proposed method has been evaluated on three different datasets, a deforming synthetic dataset, hand gesture dataset and 2-photon microscopy images of dendritic spines and, according to both visual and quantitative results, it has been demonstrated that it has a successful performance in segmentation of deforming objects whose shapes come from multi-modal shape densities. Also it has been shown that the proposed method is able to handle low quality images, highly noisy images, images with data loss, and occluded images

Probabilistic procrustean models for shape recognition with an application to robotic grasping

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.Includes bibliographical references (p. 92-98).Robot manipulators largely rely on complete knowledge of object geometry in order to plan their motion and compute successful grasps. If an object is fully in view, the object geometry can be inferred from sensor data and a grasp computed directly. If the object is occluded by other entities in the scene, manipulations based on the visible part of the object may fail; to compensate, object recognition is often used to identify the location of the object and compute the grasp from a prior model. However, new instances of a known class of objects may vary from the prior model, and known objects may appear in novel configurations if they are not perfectly rigid. As a result, manipulation can pose a substantial modeling challenge when objects are not fully in view. In this thesis, we will attempt to model the shapes of objects in a way that is robust to both deformations and occlusions. In addition, we will develop a model that allows us to recover the hidden parts of occluded objects (shape completion), and which maintains information about the object boundary for use in robotic grasp planning. Our approach will be data-driven and generative, and we will base our probabilistic models on Kendall's Procrustean theory of shape.by Jared Marshall Glover.S.M

Spatial Pyramid Context-Aware Moving Object Detection and Tracking for Full Motion Video and Wide Aerial Motion Imagery

A robust and fast automatic moving object detection and tracking system is essential to characterize target object and extract spatial and temporal information for different functionalities including video surveillance systems, urban traffic monitoring and navigation, robotic. In this dissertation, I present a collaborative Spatial Pyramid Context-aware moving object detection and Tracking system. The proposed visual tracker is composed of one master tracker that usually relies on visual object features and two auxiliary trackers based on object temporal motion information that will be called dynamically to assist master tracker. SPCT utilizes image spatial context at different level to make the video tracking system resistant to occlusion, background noise and improve target localization accuracy and robustness. We chose a pre-selected seven-channel complementary features including RGB color, intensity and spatial pyramid of HoG to encode object color, shape and spatial layout information. We exploit integral histogram as building block to meet the demands of real-time performance. A novel fast algorithm is presented to accurately evaluate spatially weighted local histograms in constant time complexity using an extension of the integral histogram method. Different techniques are explored to efficiently compute integral histogram on GPU architecture and applied for fast spatio-temporal median computations and 3D face reconstruction texturing. We proposed a multi-component framework based on semantic fusion of motion information with projected building footprint map to significantly reduce the false alarm rate in urban scenes with many tall structures. The experiments on extensive VOTC2016 benchmark dataset and aerial video confirm that combining complementary tracking cues in an intelligent fusion framework enables persistent tracking for Full Motion Video and Wide Aerial Motion Imagery.Comment: PhD Dissertation (162 pages

Nonparametric statistical methods for image segmentation and shape analysis

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Page 131 blank.Includes bibliographical references (p. 125-130).Image segmentation, the process of decomposing an image into meaningful regions, is a fundamental problem in image processing and computer vision. Recently, image segmentation techniques based on active contour models with level set implementation have received considerable attention. The objective of this thesis is in the development of advanced active contour-based image segmentation methods that incorporate complex statistical information into the segmentation process, either about the image intensities or about the shapes of the objects to be segmented. To this end, we use nonparametric statistical methods for modeling both the intensity distributions and the shape distributions. Previous work on active contour-based segmentation considered the class of images in which each region can be distinguished from others by second order statistical features such as the mean or variance of image intensities of that region. This thesis addresses the problem of segmenting a more general class of images in which each region has a distinct arbitrary intensity distribution. To this end, we develop a nonparametric information-theoretic method for image segmentation. In particular, we cast the segmentation problem as the maximization of the mutual information between the region labels and the image pixel intensities. The resulting curve evolution equation is given in terms of nonparametric density estimates of intensity distributions, and the segmentation method can deal with a variety of intensity distributions in an unsupervised fashion. The second component of this thesis addresses the problem of estimating shape densities from training shapes and incorporating such shape prior densities into the image segmentation process.(cont.) To this end, we propose nonparametric density estimation methods in the space of curves and the space of signed distance functions. We then derive a corresponding curve evolution equation for shape-based image segmentation. Finally, we consider the case in which the shape density is estimated from training shapes that form multiple clusters. This case leads to the construction of complex, potentially multi-modal prior densities for shapes. As compared to existing methods, our shape priors can: (a) model more complex shape distributions; (b) deal with shape variability in a more principled way; and (c) represent more complex shapes.by Junmo Kim.Ph.D

State of the Art of Level Set Methods in Segmentation and Registration of Medical Imaging Modalities

Segmentation of medical images is an important step in various applications such as visualization, quantitative analysis and image-guided surgery. Numerous segmentation methods have been developed in the past two decades for extraction of organ contours on medical images. Low-level segmentation methods, such as pixel-based clustering, region growing, and filter-based edge detection, require additional pre-processing and post-processing as well as considerable amounts of expert intervention or information of the objects of interest. Furthermore the subsequent analysis of segmented objects is hampered by the primitive, pixel or voxel level representations from those region-based segmentation. Deformable models, on the other hand, provide an explicit representation of the boundary and the shape of the object. They combine several desirable features such as inherent connectivity and smoothness, which counteract noise and boundary irregularities, as well as the ability to incorporate knowledge about the object of interest. However, parametric deformable models have two main limitations. First, in situations where the initial model and desired object boundary differ greatly in size and shape, the model must be re-parameterized dynamically to faithfully recover the object boundary. The second limitation is that it has difficulty dealing with topological adaptation such as splitting or merging model parts, a useful property for recovering either multiple objects or objects with unknown topology. This difficulty is caused by the fact that a new parameterization must be constructed whenever topology change occurs, which requires sophisticated schemes. Level set deformable models, also referred to as geometric deformable models, provide an elegant solution to address the primary limitations of parametric deformable models. These methods have drawn a great deal of attention since their introduction in 1988. Advantages of the contour implicit formulation of the deformable model over parametric formulation include: (1) no parameterization of the contour, (2) topological flexibility, (3) good numerical stability, (4) straightforward extension of the 2D formulation to n-D. Recent reviews on the subject include papers from Suri. In this chapter we give a general overview of the level set segmentation methods with emphasize on new frameworks recently introduced in the context of medical imaging problems. We then introduce novel approaches that aim at combining segmentation and registration in a level set formulation. Finally we review a selective set of clinical works with detailed validation of the level set methods for several clinical applications

Image segmentation with variational active contours

An important branch of computer vision is image segmentation. Image segmentation aims at extracting meaningful objects lying in images either by dividing images into contiguous semantic regions, or by extracting one or more specific objects in images such as medical structures. The image segmentation task is in general very difficult to achieve since natural images are diverse, complex and the way we perceive them vary according to individuals. For more than a decade, a promising mathematical framework, based on variational models and partial differential equations, have been investigated to solve the image segmentation problem. This new approach benefits from well-established mathematical theories that allow people to analyze, understand and extend segmentation methods. Moreover, this framework is defined in a continuous setting which makes the proposed models independent with respect to the grid of digital images. This thesis proposes four new image segmentation models based on variational models and the active contours method. The active contours or snakes model is more and more used in image segmentation because it relies on solid mathematical properties and its numerical implementation uses the efficient level set method to track evolving contours. The first model defined in this dissertation proposes to determine global minimizers of the active contour/snake model. Despite of great theoretic properties, the active contours model suffers from the existence of local minima which makes the initial guess critical to get satisfactory results. We propose to couple the geodesic/geometric active contours model with the total variation functional and the Mumford-Shah functional to determine global minimizers of the snake model. It is interesting to notice that the merging of two well-known and "opposite" models of geodesic/geometric active contours, based on the detection of edges, and active contours without edges provides a global minimum to the image segmentation algorithm. The second model introduces a method that combines at the same time deterministic and statistical concepts. We define a non-parametric and non-supervised image classification model based on information theory and the shape gradient method. We show that this new segmentation model generalizes, in a conceptual way, many existing models based on active contours, statistical and information theoretic concepts such as mutual information. The third model defined in this thesis is a variational model that extracts in images objects of interest which geometric shape is given by the principal components analysis. The main interest of the proposed model is to combine the three families of active contours, based on the detection of edges, the segmentation of homogeneous regions and the integration of geometric shape prior, in order to use simultaneously the advantages of each family. Finally, the last model presents a generalization of the active contours model in scale spaces in order to extract structures at different scales of observation. The mathematical framework which allows us to define an evolution equation for active contours in scale spaces comes from string theory. This theory introduces a mathematical setting to process a manifold such as an active contour embedded in higher dimensional Riemannian spaces such as scale spaces. We thus define the energy functional and the evolution equation of the multiscale active contours model which can evolve in the most well-known scale spaces such as the linear or the curvature scale space