Abstract The automatic reconstruction of single neuron cells from microscopic images is essential to enabling large-scale data-driven investigations in neuron morphology research. However, few previous methods were able to generate satisfactory results automatically from 3D microscopic images without human intervention. In this study, we developed a new algorithm for automatic 3D neuron reconstruction. The main idea of the proposed algorithm is to iteratively track backwards from the potential neuronal termini to the soma centre. An online confidence score is computed to decide if a tracing iteration should be stopped and discarded from the final reconstruction. The performance improvements comparing to the previous methods are mainly introduced by a more accurate estimation of the traced area and the confidence controlled back-tracking algorithm. The proposed algorithm supports large-scale batch-processing by requiring only one hyper-parameter for background segmentation. We bench-tested the proposed algorithm on the images obtained from both the DIADEM challenge and the BigNeuron challenge. Our proposed algorithm achieved the state-of-the-art results.

Automated 3D Neuron Tracing with Precise Branch Erasing and Confidence Controlled Back-Tracking