1. Brain image data processing using collaborative data workflows on Texera.
- Author
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Ding, Yunyan, Huang, Yicong, Gao, Pan, Thai, Andy, Chilaparasetti, Atchuth, Gopi, M, Xu, Xiangmin, and Li, Chen
- Subjects
3D visualization ,TissueCyte ,circuit tracing ,data analytics ,image stitching ,mouse brain ,Animals ,Brain ,Mice ,Workflow ,Imaging ,Three-Dimensional ,Image Processing ,Computer-Assisted ,Software - Abstract
In the realm of neuroscience, mapping the three-dimensional (3D) neural circuitry and architecture of the brain is important for advancing our understanding of neural circuit organization and function. This study presents a novel pipeline that transforms mouse brain samples into detailed 3D brain models using a collaborative data analytics platform called Texera. The user-friendly Texera platform allows for effective interdisciplinary collaboration between team members in neuroscience, computer vision, and data processing. Our pipeline utilizes the tile images from a serial two-photon tomography/TissueCyte system, then stitches tile images into brain section images, and constructs 3D whole-brain image datasets. The resulting 3D data supports downstream analyses, including 3D whole-brain registration, atlas-based segmentation, cell counting, and high-resolution volumetric visualization. Using this platform, we implemented specialized optimization methods and obtained significant performance enhancement in workflow operations. We expect the neuroscience community can adopt our approach for large-scale image-based data processing and analysis.
- Published
- 2024