L-systems from 3D-imaging of Phenotypes of Arborized Structures

• Autorzy: Verbeek Fons J. , Cao Lu

Identyfikatory

DOI

10.3233/FI-2020-1959

• Języki publikacji: EN

Abstrakty

EN

Biology is 3D. Therefore, it is important to be able to analyze phenomena in a spatio-temporal manner. Different fields in computational sciences are useful for analysis in biology; i.e. image analysis, pattern recognition and machine learning. To fit an empirical model to a higher abstraction, however, theoretical computer science methods are probed. We explore the construction of empirical 3D graphical models and develop abstractions from these models in L-systems. These systems are provided with a profound formalization in a grammar allowing generalization and exploration of mathematical structures in topologies. The connections between these computational approaches are illustrated by a case study of the development of the lactiferous duct in mice and the phenotypical effects from different environmental conditions we can observe on it. We have constructed a workflow to get 3D models from different experimental conditions and use these models to extract features. Our aim is to construct an abstraction of these 3D models to an L-system from features that we have measured. From our measurements we can make the productions for an L-system. In this manner we can formalize the arborization of the lactiferous duct under different environmental conditions and capture different observations. All considered, this paper illustrates the joint of empirical with theoretical computational sciences and the augmentation of the interpretation of the results. At the same time, it shows a method to analyze complex 3D topologies and produces archetypes for developmental configurations.

Słowa kluczowe

EN

3D model representation; center-line topology; L-system; lactiferous duct; phenotype analysis

• Wydawca: IOS Press
• Czasopismo: Fundamenta Informaticae
• Rocznik: 2020
• Tom: Vol. 175, nr 1-4
• Strony: 327--345
• Opis fizyczny: Bibliogr. 37 poz., rys., tab.

Twórcy

autor

Verbeek Fons J.

• Imaging and Bioinformatics group, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands

autor

Cao Lu

• Imaging and Bioinformatics group, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands

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Uwagi

Opracowanie rekordu ze środków MNiSW, umowa Nr 461252 w ramach programu "Społeczna odpowiedzialność nauki" - moduł: Popularyzacja nauki i promocja sportu (2020).