2021/06/01 by Qiufu Li, Linlin Shen, Li, Qiufu +1
Biochemistry, Genetics and Molecular Biology · Computer Science · Engineering · #Advanced Fluorescence Microscopy Techniques #Cell Image Analysis Techniques #Computer Vision and Pattern Recognition (cs.CV) #FOS: Computer and information sciences #FOS: Electrical engineering #Image Processing Techniques and Applications #Image and Video Processing (eess.IV) #cs.CV #eess.IV #electronic engineering #information engineering
paper · pdf · doi:10.48550/arxiv.2106.00259
Bioinformatics accepted paper
openalex publication_date 2021/06/01 · arxiv created 2021/11/08 · arxiv updated 2021/11/09 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Motivation: 3D neuron segmentation is a key step for the neuron digital reconstruction, which is essential for exploring brain circuits and understanding brain functions. However, the fine line-shaped nerve fibers of neuron could spread in a large region, which brings great computational cost to the neuron segmentation. Meanwhile, the strong noises and disconnected nerve fibers bring great challenges to the task. Results: In this paper, we propose a 3D wavelet and deep learning based 3D neuron segmentation method. The neuronal image is first partitioned into neuronal cubes to simplify the segmentation task. Then, we design 3D WaveUNet, the first 3D wavelet integrated encoder-decoder network, to segment the nerve fibers in the cubes; the wavelets could assist the deep networks in suppressing data noises and connecting the broken fibers. We also produce a Neuronal Cube Dataset (NeuCuDa) using the biggest available annotated neuronal image dataset, BigNeuron, to train 3D WaveUNet. Finally, the nerve fibers segmented in cubes are assembled to generate the complete neuron, which is digitally reconstructed using an available automatic tracing algorithm. The experimental results show that our neuron segmentation method could completely extract the target neuron in noisy neuronal images. The integrated 3D wavelets can efficiently improve the performance of 3D neuron segmentation and reconstruction. Availability: The data and codes for this work are available at https://github.com/LiQiufu/3D-WaveUNet.