MBI Videos

Videos by Workshop 2: Morphogenesis, Regeneration, and the Analysis of Shape

  • Data Driven Methods for Shape Analysis and Visualization
    Ross Whitaker

    Data Driven Methods for Shape Analysis and Visualization

  • Shape Analysis for Biomedical Applications
    Cindy Grimm

    Shape and function are intricately related in biology. We present three biological case studies where the goal is to quantify shape change in order to analyze how shape informs function. The biologists have specific questions they are interested in answering, and have domain knowledge that should be incorporated into the the shape correspondence algorithm. We show...

  • The Role of Imaging in Phenotypic Screening
    Jens Rittscher

    To set the stage I will introduce the phenotypic screening and the relevance of this approach to drug discovery. The talk will highlight a number of image analysis techniques that play an increasingly important role in phenotypic screening. In particular it will review algorithms for cell tracking and cell cycle estimation as well as image analysis based approache...

  • Geometric algorithms for shapes and trajectories
    Carola Wenk

    This talk will give an introduction to geometric algorithms for comparing and matching discrete geometric shapes such as point sets, polygonal curves, and graphs. We will study distance measures for shapes, approaches for matching shapes under transformations, and a...

  • 3D Actin Network Centerline Extraction with Multiple Active Contours
    Xiaolei (Sharon) Huang

    Fluorescence microscopy is frequently used to study two and three dimensional network structures formed by cytoskeletal polymer fibers such as actin filaments and actin cables. While these cytoskeletal structures are often dilute enough to allow imaging of individual filaments or bundles of them, quantitative analysis of these images is challenging. To facilitate ...

  • Probabilistic Modeling of Shape
    Tom Fletcher

    Probabilistic Modeling of Shape

  • Gut patterning, brain gyrification and wing shape
    L. Mahadevan

    Gut patterning, brain gyrification and wing shape.

  • Metric-Based Approaches for shape analysis
    Anuj Srivastava

    Shape analysis of objects intrinsically involves registration of points across objects. While registration is historically treated as a pre-processing step, a more recent trend is to incorporate it as an integral step in shape comparison. There are two distinct approaches for shape registration -- model based and metric based.

    (1) In the ...

  • A distance on curves using orthogonal transformations
    Jaap Eldering

    We construct a geometric method to directly quantify the difference between curves. That is, we construct a distance for parametrized curves in R^n modulo Euclidean transformations. This distance measures the local dissimilarity of k-jets (Taylor polynomials) of the curves. The distance is obtained from a variational principle, and can be constructed by solving a bounda...

  • Airway tree-shape modeling through large-scale tree-space statistics
    Aasa Feragen

    Anatomical trees appear as transportation systems distributing blood, water or air. Due to their critical role, statistics on populations of trees is essential to understanding disease. This is difficult due to anatomical variation in branching structure across subjects. I will present a geometric tree-space framework for leaf-labeled trees, discuss how statistics can b...

  • Diffeomorphometry of f-shapes
    Alain Trouve

    Shape spaces have emerged as a natural mathematical setting to think about shapes as a structured space. In that setting, group actions of diffeomorphisms provide nice vehicles to build a full processing framework called here diffeomorphometry. This talks will present a recently developed framework embedding the situation of geometrical shapes carrying a functiona...

  • Cell Shape Determination in Single-Cell Motility
    Julie Theriot

    Julie Thierot's talk onCell Shape Determination in Single-Cell Motility

  • Inner ear size and shape is regulated by pressure, transport, and tissue mechanics
    Kishore Rao Mosaliganti

    How do animals develop similar organ sizes and shapes despite large fluctuations in initial growth conditions? How is size and shape control achieved across molecular-cellular-tissue scales? We answer this question in the context of early ear development that exhibits a highly stereotyped pattern of assembly and growth. Using in toto imaging technologies in the ze...

  • Unpacking neuronal form and neighborhoods from connectomes
    Robert Marc

    Mapping neural networks in brain, retina and spinal cord requires (1) comprehensive parts lists (vertex types), (2) nanometer scale connection detection (edge types), and (3) millimeter scale network tracing. Connectomics based on high-resolution automated transmission electron microscope imaging merges these operations and allows discovery of network modules and ...

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