skip to main content

This content will become publicly available on March 28, 2023

Title: Characterizing Cell Populations Using Statistical Shape Modes
We consider the problem of characterizing shape populations using highly frequent representative shapes. Framing such shapes as statistical modes – shapes that correspond to (significant) local maxima of the underlying pdfs – we develop a frequency-based, nonparametric approach for estimating sample modes. Using an elastic shape metric, we define ϵ-neighborhoods in the shape space and shortlist shapes that are central and have the most neighbors. A critical issue – How to automatically select the threshold ϵ? – is resolved using a combination of ANOVA and empirical mode distribution. The resulting modal set, in turn, helps characterize the shape population and performs better than the traditional cluster means. We demonstrate this framework using amoeba shapes from brightfield microscopy images and highlight its advantages over existing ideas.
Authors:
; ; ; ;
Award ID(s):
1953087 1955154
Publication Date:
NSF-PAR ID:
10339549
Journal Name:
2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI)
Page Range or eLocation-ID:
1 to 5
Sponsoring Org:
National Science Foundation
More Like this
  1. Background Comparative morphology fundamentally relies on the orientation and alignment of specimens. In the era of geometric morphometrics, point-based homologies are commonly deployed to register specimens and their landmarks in a shared coordinate system. However, the number of point-based homologies commonly diminishes with increasing phylogenetic breadth. These situations invite alternative, often conflicting, approaches to alignment. The bivalve shell (Mollusca: Bivalvia) exemplifies a homologous structure with few universally homologous points—only one can be identified across the Class, the shell ‘beak’. Here, we develop an axis-based framework, grounded in the homology of shell features, to orient shells for landmark-based, comparative morphology. Methods Using 3D scans of species that span the disparity of shell morphology across the Class, multiple modes of scaling, translation, and rotation were applied to test for differences in shell shape. Point-based homologies were used to define body axes, which were then standardized to facilitate specimen alignment via rotation. Resulting alignments were compared using pairwise distances between specimen shapes as defined by surface semilandmarks. Results Analysis of 45 possible alignment schemes finds general conformity among the shape differences of ‘typical’ equilateral shells, but the shape differences among atypical shells can change considerably, particularly those with distinctive modes of growth. Eachmore »alignment corresponds to a hypothesis about the ecological, developmental, or evolutionary basis of morphological differences, but we suggest orientation via the hinge line for many analyses of shell shape across the Class, a formalization of the most common approach to morphometrics of shell form. This axis-based approach to aligning specimens facilitates the comparison of approximately continuous differences in shape among phylogenetically broad and morphologically disparate samples, not only within bivalves but across many other clades.« less
  2. Abstract

    Bivalves protect themselves from predators using both mechanical and behavioral defenses. While their shells serve as mechanical armor, bivalve shells also enable evasive behaviors such as swimming and burrowing. Therefore, bivalve shell shape is a critical determinant of how successfully an organism can defend against attack. Shape is believed to be related to shell strength with bivalve shell shapes converging on a select few morphologies that correlate with life mode and motility. In this study, mathematical modeling and 3D printing were used to analyze the protective function of different shell shapes against vertebrate shell-crushing predators. Considering what life modes different shapes permit and analyzing the strength of these shapes in compression provides insight to evolutionary and ecological tradeoffs with respect to mechanical and behavioral defenses. These empirical tests are the first of their kind to isolate the influence of bivalve shell shape on strength and quantitatively demonstrate that shell strength is derived from multiple shape parameters. The findings of this theoretical study are consistent with examples of shell shapes that allow escape behaviors being mechanically weaker than those which do not. Additionally, shell elongation from the umbo, a metric often overlooked, is shown to have significant effects on shell strength.

  3. Murphy, William (Ed.)
    Abstract Organisms across the tree of life have complex life cycles that include both sexual and asexual reproduction or that are obligately asexual. These organisms include ecologically dominant species that structure many terrestrial and marine ecosystems, as well as many pathogens, pests, and invasive species. We must consider both the evolution and maintenance of these various reproductive modes and how these modes shape the genetic diversity, adaptive evolution, and ability to persist in the species that exhibit them. Thus, having a common framework is a key aspect of understanding the biodiversity that shapes our planet. In the 2019 AGA President’s Symposium, Sex and Asex: The genetics of complex life cycles, researchers investigating a wide range of taxonomic models and using a variety of modes of investigation coalesced around a common theme—understanding not only how such complex life cycles may evolve, but how they are shaped by the evolutionary and ecological forces around them. In this introduction to the Special Issue from the symposium, we give an overview of some of the key ideas and areas of investigation (a common clonal lexicon, we might say) and introduce the breadth of work submitted by symposium participants.
  4. Abstract

    The ignition of plasmas in liquids has applications from medical instrumentation to manipulation of liquid chemistry. Formation of plasmas directly in a liquid often requires prohibitively large voltages to initiate breakdown. Producing plasma streamers in bubbles submerged in a liquid with higher permittivity can significantly lower the voltage needed to initiate a discharge by reducing the electric field required to produce breakdown. The proximity of the bubble to the electrodes and the shape of the bubbles play critical roles in the manner in which the plasma is produced in, and propagates through, the bubble. In this paper, we discuss results from a three-dimensional direct numerical simulation (DNS) used to investigate the shapes of bubbles formed by injection of air into water. Comparisons are made to results from a companion experiment. A two-dimensional plasma hydrodynamics model was then used to capture the plasma streamer propagation in the bubble using a static bubble geometry generated by the DNS The simulations showed two different modes for streamer formation depending on the bubble shape. In an elliptical bubble, a short electron avalanche triggered a surface ionization wave (SIWs) resulting in plasma propagating along the surface of the bubble. In a circular bubble, anmore »electron avalanche first traveled through the middle of the bubble before two SIWs began to propagate from the point closest to the grounded electrode where a volumetric streamer intersected the surface. In an elliptical bubble approaching a powered electrode in a pin-to-pin configuration, we experimentally observed streamer behavior that qualitatively corresponds with computational results. Optical emission captured over the lifetime of the streamer curve along the path of deformed bubbles, suggesting propagation of the streamer along the liquid/gas boundary interface. Plasma generation supported by the local field enhancement of the deformed bubble surface boundaries is a mechanism that is likely responsible for initiating streamer formation.

    « less
  5. Abstract Morphing structures, defined as body panels that are capable of a drastic autonomous shape transformation, have gained importance in the aerospace, automotive, and soft robotics industries since they address the need to switch between shapes for optimal performance over the range of operation. Laminated composites are attractive for morphing because multiple laminae, each serving a specific function, can be combined to address multiple functional requirements such as shape transformation, structural integrity, safety, aerodynamic performance, and minimal actuation energy. This paper presents a review of laminated composite designs for morphing structures. The trends in morphing composites research are outlined and the literature on laminated composites is categorized based on deformation modes and multifunctional approaches. Materials commonly used in morphing structures are classified based on their properties. Composite designs for various morphing modes such as stretching, flexure, and folding are summarized and their performance is compared. Based on the literature, the laminae in an n-layered composite are classified based on function into three types: constraining, adaptive, and prestressed. A general analytical modeling framework is presented for composites comprising the three types of functional laminae. Modeling developments for each morphing mode and for actuation using smart material-based active layers are discussed. Results,more »presented for each deformation mode, indicate that the analytical modeling can not only provide insight into the structure's mechanics but also serve as a guide for geometric design and material selection.« less