Retrieving similar substructures on 3D neuron reconstructions

• Main Authors: Jian Yang, Yishan He, Xuefeng Liu
• Format: Article
• Language: English
• Published: SpringerOpen 2020-11-01
• Series: Brain Informatics
• Subjects: Neuronal morphology; Reconstruction; Substructure; Retrieving
• Online Access: http://link.springer.com/article/10.1186/s40708-020-00117-x

Abstract Since manual tracing is time consuming and the performance of automatic tracing is unstable, it is still a challenging task to generate accurate neuron reconstruction efficiently and effectively. One strategy is generating a reconstruction automatically and then amending its inaccurate parts manually. Aiming at finding inaccurate substructures efficiently, we propose a pipeline to retrieve similar substructures on one or more neuron reconstructions, which are very similar to a marked problematic substructure. The pipeline consists of four steps: getting a marked substructure, constructing a query substructure, generating candidate substructures and retrieving most similar substructures. The retrieval procedure was tested on 163 gold standard reconstructions provided by the BigNeuron project and a reconstruction of a mouse’s large neuron. Experimental results showed that the implementation of the proposed methods is very efficient and all retrieved substructures are very similar to the marked one in numbers of nodes and branches, and degree of curvature.