Shape Modeling of Plant Leaves with Unstructured Meshes

The plant leaf is one of the most challenging natural objects to be realistically depicted by computer graphics due to its complex morphological and optical characteristics. Although many studies have been done on plant modeling, previous research on leaf modeling required for close-up realistic plant images is very rare. In this thesis, a novel method for modeling of the leaf shape based on the leaf venation is presented. As the first step of the method, the leaf domain is defined by the enclosure of the leaf boundary. Second, the leaf venation is interactively modeled as a hierarchical skeleton based on the actual leaf image. Third, the leaf domain is triangulated with the skeleton as constraints. The skeleton is articulated with nodes on the skeleton. Fourth, the skeleton is interactively transformed to a specific shape. A user can manipulate the skeleton using two methods which are complementary to each other: one controls individual joints on the skeleton while the other controls the skeleton through an intermediate spline curve. Finally, the leaf blade shape is deformed to conform to the skeleton by interpolation. An interactive modeler was developed to help a user to model a leaf shape interactively and several leaves were modeled by the interactive modeler. The ray-traced rendering images demonstrate that the proposed method is effective in the leaf shape modeling

Space colonisation based procedural road generation

Dissertação de mestrado em Computer ScienceProcedural generation of content has been studied for quite some time and it is increasingly relevant in scientific areas and in video-game and film industries. Procedural road layout generation has been traditionally approached using L-Systems, with some works exploring alternative avenues. Although originally conceived for biological systems modelling, the adequacy of L-Systems as a base for road generation has been demonstrated in several works. In this context, this work presents an alternative approach for procedural road layout generation that is also inspired by plant generation algorithms: space colonisation. In particular, this work uses the concept of attraction points introduced in space colonisation as its base to produce road layouts, both in urban and inter-city environments. As will be shown, the usage of attraction points provides an intuitive way to parameterise a road layout. The original Space Colonization Algorithm (SCA) generates a tree like structure, but in this work, the extensions made aim to fully generate a inter-connected road network. As most previous methods the method has two phases. A first phase generates what is mostly a tree structure growing from user defined road segments. The second phase performs the inter connectivity among the roads created in the first phase. The original SCA parameters such as the killradius help to control the capillarity of the road layout, the number of attraction points used by each segment will dictate its relevance establishing a road hierarchy naturally dependent on the distribution of the attraction points on the terrain. An angle control allows the creation of grid like or more organic road layouts. The distribution of the attraction points in the terrain can be conditioned by boundary maps, containing parks, sea, rivers, and other forbidden areas. Population density maps can be used to supply an explicit probabilistic distribution to the attraction points. Flow-fields can be used to dictate the flow of the road layout. Elevation maps provide an additional restriction regarding the steepness of the roads. The tests were executed within a graphic toolbox developed simultaneously. The results are exported to a geographical information file format, GeoJSON, and then maps are rendered using a geospatial visualisation and processing framework called Mapnik. For the most part, parameter settings were intuitively reflected on the road layout and this method can be seen as a first step towards fully exploring the usage of attraction points in the context of road layout.Gradualmente a geração procedimental de conteúdo tem-se tornado cada vez mais relevante, sendo maioritariamente aplicada em industrias como a dos vídeo-jogos e cinema. No que toca à geração procedimental de redes de estradas, grande parte das abordagens em torno deste tema são baseadas em L-Systems. Embora a área de aplicação dos L-Systems tenha sido originalmente para produzir modelos de sistemas biológicos, mostrou também ser um algoritmo adequado para a geração procedimental de redes de estradas. Este trabalho apresenta uma abordagem alternativa à geração procedimental de redes de estradas que também é inspirada num algoritmo procedimental de geração de plantas, colonização espacial, utilizando o conceito de pontos de atracão como base para gerar padrões de estradas. Como será demonstrado, a utilização de pontos de atracão fornece uma maneira intuitiva de parametrizar um padrão de estradas desejado. Como a maioria dos trabalhos feitos nesta área, este método tem duas fases. A primeira fase gera uma rede semelhante a uma árvore criada a partir de um ou mais segmentos iniciais da rede determinados pelo utilizador. A segunda fase trata de interligar as estradas geradas na primeira fase. Os parâmetros iniciais do algoritmo de colonização espacial, como o kill radius, ajudam a controlar a capilaridade da rede, os pontos de atracão que influenciam cada segmento irão ditar a sua relevância na rede geral, estabelecendo a noção de hierarquia de estradas, dependendo da distribuição de pontos de atracão no terreno. O controlo do ângulo entre segmentos permite a criação de padrões de estradas tanto em forma de grelha como padrões mais orgânicos. A distribuição dos pontos de atracão no terreno pode ser influenciada por mapas de fronteira, que contem as áreas válidas e/ou inválidas, como parques, mar, rios, e outras áreas proibidas. Mapas de densidade populacional podem ser usados para fornecer uma distribuição probabilística dos pontos de atracão. Campos de forças, podem ser usados para ditar o fluxo da rede de estradas. Mapas de elevação oferecem uma restrição adicional tendo em conta a inclinação das estradas. De um modo geral, as definições de parâmetros refletiram-se de um modo intuitivo nos padrões de redes de estradas gerados, e este trabalho pode ser considerado como um primeiro passo na exploração do conceito de pontos de atracão na área da geração de redes de estradas

Procedural Modeling and Constrained Morphing of Leaves

Ph.DDOCTOR OF PHILOSOPH

Modeling auxin feedback signaling for polarized auxin transport in plant development

Plants are fascinating biological systems with a great potential for adaption of their developmental programs to environmental cues. In contrast to animals, plants cannot run away and thus they had to develop specialized mechanisms to react to rapid changes in the environment. These plant-specific mechanisms including light perception, tropism and developmental reprogramming (de novo organ formation, tissue re-shaping), represent highly dynamic regulatory processes that are linked and intertwined on the molecular, cellular and tissue levels. The ultimate communication between these different levels is the key to understand how plants realize their developmental decisions. Cell signaling, tissue polarization, directional transport of signaling molecules within tissues are among those biological processes that allow for such multilevel organization in plant development. Nevertheless our understanding of these processes remains largely elusive. This doctoral thesis demonstrates the results of multidisciplinary studies at the interface between several scientific disciplines, including mathematics, computer science (under supervision of Prof. Willy Govaerts) and cell and developmental biology (under guidance of Prof. Jiří Friml). Therefore, I will utilize state-of-the-art mathematical and computational techniques combined with the most recent biological data to address cell and tissue polarities as well as graded distribution patterns of the plant phytohormone auxin, in the context of plant developmental flexibility. The main goal of the research presented herein was to explore general principles of auxin feedback regulation and its outstanding roles in auxin-driven plant development. A special focus was given to the combination of local auxin signaling cues (inside and outside of the cell), subcellular dynamics (trafficking of auxin carriers) and cell-type specific factors (spatial patterns of gene activity) to account for the developmental patterns observed in planta such as canalization of auxin transport, leaf venation patterning, tissue regeneration and establishment and maintenance of cell and tissue polarities. The core of the thesis will start with a general introduction to the models for auxin-mediated plant development and will be followed by presentation of various scientific results and their potential implications for hopefully better understanding of patterning mechanisms in plants. Finally, the summarizing chapter of this thesis aims to translate the results of these various studies to the more general concept of the local auxin feedback regulation in plants

Evaluating NeRFs for 3D Plant Geometry Reconstruction in Field Conditions

We evaluate different Neural Radiance Fields (NeRFs) techniques for reconstructing (3D) plants in varied environments, from indoor settings to outdoor fields. Traditional techniques often struggle to capture the complex details of plants, which is crucial for botanical and agricultural understanding. We evaluate three scenarios with increasing complexity and compare the results with the point cloud obtained using LiDAR as ground truth data. In the most realistic field scenario, the NeRF models achieve a 74.65% F1 score with 30 minutes of training on the GPU, highlighting the efficiency and accuracy of NeRFs in challenging environments. These findings not only demonstrate the potential of NeRF in detailed and realistic 3D plant modeling but also suggest practical approaches for enhancing the speed and efficiency of the 3D reconstruction process.This is a preprint from Arshad, Muhammad Arbab, Talukder Jubery, James Afful, Anushrut Jignasu, Aditya Balu, Baskar Ganapathysubramanian, Soumik Sarkar, and Adarsh Krishnamurthy. "Evaluating NeRFs for 3D Plant Geometry Reconstruction in Field Conditions." arXiv preprint arXiv:2402.10344 (2024). doi: https://doi.org/10.48550/arXiv.2402.10344. Copyright 2023 The Authors

Constructing living buildings: a review of relevant technologies for a novel application of biohybrid robotics

Biohybrid robotics takes an engineering approach to the expansion and exploitation of biological behaviours for application to automated tasks. Here, we identify the construction of living buildings and infrastructure as a high-potential application domain for biohybrid robotics, and review technological advances relevant to its future development. Construction, civil infrastructure maintenance and building occupancy in the last decades have comprised a major portion of economic production, energy consumption and carbon emissions. Integrating biological organisms into automated construction tasks and permanent building components therefore has high potential for impact. Live materials can provide several advantages over standard synthetic construction materials, including self-repair of damage, increase rather than degradation of structural performance over time, resilience to corrosive environments, support of biodiversity, and mitigation of urban heat islands. Here, we review relevant technologies, which are currently disparate. They span robotics, self-organizing systems, artificial life, construction automation, structural engineering, architecture, bioengineering, biomaterials, and molecular and cellular biology. In these disciplines, developments relevant to biohybrid construction and living buildings are in the early stages, and typically are not exchanged between disciplines. We, therefore, consider this review useful to the future development of biohybrid engineering for this highly interdisciplinary application.publishe