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    Center for Computational and Theoretical Biology

    Summary

    We use image analysis, topological quantification and growth modeling to understand the mechanisms behind the development and function of spatial biological networks.

    Details

    Image Analysis

    We develop novel methods to extract curvilinear structures from 3D microscopy images, and to derive their skeleton and topological structure.

    Modeling

    By simulating the growth of spatial networks under different assumptions, we want to understand the relationship between local growth rules and global network connectivity.

    Code and Data

    1. MATLAB code for 3D skeletonization:

    https://github.com/phi-max/skeleton3d-matlab

    2. MATLAB code for 3D skeleton-to-graph conversion:

      https://github.com/phi-max/skel2graph3d-matlab

    3. MATLAB code and data to reproduce the figures from the "Osteocyte Connectomics" paper (New Journal of Physics 2017):

      https://github.com/phi-max/OCY_connectomics (Code)

      https://zenodo.org/record/291852 (Data)

    4. Tool for Image and Network Analysis (TINA) - Python code developed by Felix Repp during his PhD thesis at the MPIKG and used in the two papers by Repp et al. (Bone Reports 2017 and Journal of Structural Biology 2017):

      https://bitbucket.org/refelix/tina

    Contact

    Center for Computational and Theoretical Biology
    Gebäude 32
    Campus Hubland Nord
    97074 Würzburg

    Find Contact

    Hubland Nord, Geb. 32