AUTHOR=Ding Yunyan , Huang Yicong , Gao Pan , Thai Andy , Chilaparasetti Atchuth Naveen , Gopi M. , Xu Xiangmin , Li Chen TITLE=Brain image data processing using collaborative data workflows on Texera JOURNAL=Frontiers in Neural Circuits VOLUME=18 YEAR=2024 URL=https://www.frontiersin.org/journals/neural-circuits/articles/10.3389/fncir.2024.1398884 DOI=10.3389/fncir.2024.1398884 ISSN=1662-5110 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.