Neuron Image Segmentation via Learning Deep Features and Enhancing Weak Neuronal Structures

Neuron morphology reconstruction (tracing) in 3D volumetric images is critical for neuronal research. However, most existing neuron tracing methods are not applicable in challenging datasets where the neuron images are contaminated by noises or containing weak filament signals. In this paper, we present a two-stage 3D neuron segmentation approach via learning deep features and enhancing weak neuronal structures, to reduce the impact of image noise in the data and enhance the weak-signal neuronal structures. In the first stage, we train a voxel-wise multi-level fully convolutional network (FCN), which specializes in learning deep features, to obtain the 3D neuron image segmentation maps in an end-to-end manner. In the second stage, a ray-shooting model is employed to detect the discontinued segments in segmentation results of the first-stage, and the local neuron diameter of the broken point is estimated and direction of the filamentary fragment is detected by rayburst sampling algorithm. Then, a Hessian-repair model is built to repair the broken structures, by enhancing weak neuronal structures in a fibrous structure determined by the estimated local neuron diameter and the filamentary fragment direction. Experimental results demonstrate that our proposed segmentation approach achieves better segmentation performance than other state-of-the-art methods for 3D neuron segmentation. Compared with the neuron reconstruction results on the segmented images produced by other segmentation methods, the proposed approach gains 47.83% and 34.83% improvement in the average distance scores. The average Precision and Recall rates of the branch point detection with our proposed method are 38.74% and 22.53% higher than the detection results without segmentation.