PyNeval: A Python Toolbox for Evaluating Neuron Reconstruction Performance

• Published in: Frontiers in neuroinformatics Vol. 15; p. 767936
• Main Authors: Zhang, Han, Liu, Chao, Yu, Yifei, Dai, Jianhua, Zhao, Ting, Zheng, Nenggan
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Research Foundation 28.01.2022; Frontiers Media S.A
• Subjects: Algorithms; Design; metric; neuron reconstruction; neuron tracing; Neuroscience; PyNeval; Quality control; quantitative analysis; Software; toolbox; toolbox; neuron tracing; quantitative analysis; metric; PyNeval; neuron reconstruction
• ISSN: 1662-5196; 1662-5196
• DOI: 10.3389/fninf.2021.767936

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, with 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.