Skeleton optimization of neuronal morphology based on three-dimensional shape restrictions
Authors: Siqi Jiang, Zhengyu Pan, Zhao Feng, Yue Guan, Miao Ren, Zhangheng Ding, Shangbin Chen, Hui Gong, Qingming Luo, Anan Li*
Correspondence author: aali@mail.hust.edu.cn

Neurons are the basic structural unit of the brain, and its morphology is a key determinant with regard to its classification. Neuronal circuit, composed by neuronal morphology, is a fundamental component for neuron modeling. Previous neuron tracing methods, especially the Skeletonization methods, are designed on the pixel grid and grayscale, which may cause computation errors in the subsequent morphological analysis and neuron modelling. In this study, we propose a neuronal digital skeleton optimization method to evaluate and finely adjust the digital skeleton after the neuron tracing. Providing the neuron fiber shape is smooth and continuous, we descript this physical property as two shape restrictions. One restriction is designed based on the image grayscale, that the difference of the signal brightness between the local pixels around neuronal fiber centerline, are small. The other is designed based on geometry is gentle. These two restrictions are constrained to finely adjust the digital skeleton points to the neuronal fiber centerline. With this method, we design the three-dimensional shape restrictions workflow of neuronal skeleton adjustment computation. This method can improve the accuracy of the neuronal digital skeleton based on the traced results. Consequently, the more accurate digital skeletons are acquired, the more precise neuronal morphologies are analyzed.

Data:
Test Data1: Image stack and SWC file for skeleton optimization of axon (130MB)
Test Data2: Image stack and SWC file for skeleton optimization of dendrite (167MB)
In additional, the fMOST whole brain image dataset is over 30 TB, which is very huge that cannot be shared via internet. But, it is available from the corresponding author on reasonable request.

Source code:
Matlab language, please refer to the readme file, if you have any questions please contact us.