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DeepBrainSeg: Automated Brain Region Segmentation for Micro-Optical Images With a Convolutional Neural Network
Chaozhen Tan1,2, Yue Guan1,2, Zhao Feng1,2
1Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China.
Frontiers in Neuroscience
|April 9, 2020
Summary
DeepBrainSeg automates brain region segmentation using a dual-pathway convolutional neural network (CNN). This framework accurately maps brain structures from microscopic images, overcoming challenges of blurry boundaries and complex features.
Area of Science:
- Neuroscience
- Computational Biology
- Medical Imaging
Background:
- Accurate 3D segmentation of brain regions is crucial for neuroscience research.
- High-resolution imaging reveals cellular detail but presents segmentation challenges due to blurry boundaries and complex neuronal aggregation.
- Manual segmentation is accurate but not scalable for large datasets.
Purpose of the Study:
- To develop an automated framework, DeepBrainSeg, for accurate and scalable 3D brain region segmentation.
- To mimic manual segmentation principles using advanced computational methods.
- To improve the analysis of brain structures from large-scale microscopic imaging data.
Main Methods:
- Developed DeepBrainSeg, a dual-pathway convolutional neural network (CNN) framework.
- Incorporated three feature levels to capture local and contextual information across different receptive fields.
- Utilized image registration and domain-condition constraints for global localization features.
Main Results:
- Achieved high accuracy in brain-wide region segmentation, with Dice ratios exceeding 0.9.
- Demonstrated robustness across diverse biological datasets, including those with noise.
- Successfully applied the framework to various imaging datasets.
Conclusions:
- DeepBrainSeg provides an effective automated solution for 3D brain region segmentation.
- The framework's accuracy and versatility make it suitable for large-scale neuroscience studies.
- DeepBrainSeg facilitates automated information localization within the brain space.
