PyNeval: A Python Toolbox for Evaluating Neuron Reconstruction Performance

Han Zhang, Chao Liu, Yifei Yu, Jianhua Dai, Ting Zhao, Nenggan Zheng
2022 Frontiers in Neuroinformatics  
Quality assessment of tree-like structures obtained from a neuron reconstruction algorithm is necessary for evaluating the performance of the algorithm. The lack of user-friendly software for calculating common metrics motivated us to develop a Python toolbox called PyNeval, which is the first open-source toolbox designed to evaluate reconstruction results conveniently as far as we know. The toolbox supports popular metrics in two major categories, geometrical metrics and topological metrics,
more » ... th an easy way to configure custom parameters for each metric. We tested the toolbox on both synthetic data and real data to show its reliability and robustness. As a demonstration of the toolbox in real applications, we used the toolbox to improve the performance of a tracing algorithm successfully by integrating it into an optimization procedure.
doi:10.3389/fninf.2021.767936 pmid:35153709 pmcid:PMC8831325 fatcat:dms6ciezpfarjknhwchrkzcrni