Fig. 4: Available network reconstruction software.

a Spatial network reconstructions by cytoNet¹⁰⁵. Type I networks establish connections (yellow line) between cells (bordered in cyan) that touch when dilated. Type II networks establish connections (yellow line) between cells based on whether the distance between their nuclei (bordered in red) falls below a defined threshold. Image adapted from ref. ¹²⁶ and modified (CC BY 4.0). b ExplantAnalyzer⁶⁴ network reconstruction of spiral ganglion explant neurites (stained with β-Tubulin III and DAPI, scale bar: 1 mm). A pruned graph structure is created by finding the shortest path from each neurite end point depicted in green to the explant body attachment point depicted in red. Edges not part of any shortest paths are removed from the final tree. Figure adapted from ref. ⁶⁴ and modified (CC BY 4.0). c An example workflow of the network reconstruction tool developed by refs. ^86,90. An input brightfield image of poor quality is morphologically labelled by yolov3; blue boxes are neuron somata, yellow box is a neuron somata cluster. After segmentation, a preliminary network is reconstructed with red nodes (branch and end points), blue edges, and yellow underlying skeleton, followed by final network reconstruction. Figure adapted from ref. ⁸⁶ and modified with permission.