Morphospace: Measurement, Modeling, Mathematics, and Meaning

Abstract

Abstract. Artists have long recognized that trees are self-similar across enormous differences in magnitudes; i.e., they share a common fractal structure -a trunk subdivides into branches which subdivide into more branches which eventually terminate in leaves, flowers, fruits, etc. Artistid Lindenmayer (1971, 1975, 1989, 1990) invented a mathematics based on graph grammar rewriting systems to describe such iteratively branching structures; these were named in honor of him and are referred to as L-systems. With the advent of fractals into computer graphics, numerous artists have similarly produced a wide variety of software packages to illustrate the beauty of fractal/Lsystem generated plants. Some tree visualizations such as L-Peach (Allen et al., 2005) do depend very explicitly upon a complex set of precise measurements of a single species of tree. Nonetheless, we felt that there is a need to build a package that allowed scientists (and students) to collect data from actual specimens in the field or laboratory, insert these measurements into an L-system package, and then visually compare actual trees to the computer generated image with such specimens. Furthermore, the effect of variance in parameters helps users evaluate the developmental plasticity both within and between species and varieties. We have developed 3D FractaL Tree (the L is capitalized in honor of Lindemayer) to generate trees based upon measurement of (1) relative lengths of two successive segments averaged over several iterations, (2) the angle theta between bifurcating limbs at successive joints, (3) the number of steps in branching that one must follow to find a branch extending at the same angle as the first one under consideration to determine the phyllotactic angle phi, (4) the average of the summed areas (determined from measurement of diameters) of bifurcations compared to the trunk to determine whether area of flow is preserved (and * Corresponding author. E-mail: jungck@beloit. Morphospace: measurement, modeling, mathematics, and meaning to consider Poiseuille's/Murray's law of laminar flow in a fractal network), (5) the total number of iterative branching from the base to the tip of tree averaged over several counts based on following out different major limbs, (6) an editable L-system rule chosen from a library of branching patterns that roughly correspond to a specimen under consideration, and (7) a degree of stochasticity applied to the above rules to represent some variation over the course of a lifetime. Of course, turned upside down, the computer imagery could be used to represent root structure instead of above ground growth or the bronchial system of a lung, for example. The measurements are recorded and analyzed in a series of worksheets in Microsoft Excel and the results are entered into the graphics engine in a Java application. 3D FractaL Tree produces a rotatable three-dimensional image of the tree which is helpful for examining such characters as self-avoidance (entanglement and breakage), reception of and penetration o...

Ka-me: a Voronoi image analyzer

“…We ( Khiripet et al , 2011 ) are generally interested in articulating the close relationship between actual biological specimens and causal theoretical models. Ka-me instantiates this approach by allowing an investigator to choose among a diversity of mathematical and statistical tools for testing causal hypotheses about biological patterns.…”