The 3D skeleton was derived using the homotopic thinning algorithm described in Lee et al., 1994 specifically optimized for Matlab implementation by Kollmannsberger (Kerschnitzki et al., 2013), (online source: https://www.mathworks.com/matlabcentral/fileexchange/43400-skeleton3d). Calculated 3D medial axis skeleton was subsequently converted to a network graph, using algorithm described in Kerschnitzki et al., 2013 (online source: https://www.mathworks.com/matlabcentral/fileexchange/43527-skel2graph-3d). Resulting network graph is formed by nodes and links between them (Figure 1—figure supplement 12D and G).

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