Frontiers in Neural Circuits (Jul 2024)

Brain image data processing using collaborative data workflows on Texera

  • Yunyan Ding,
  • Yicong Huang,
  • Pan Gao,
  • Andy Thai,
  • Atchuth Naveen Chilaparasetti,
  • M. Gopi,
  • Xiangmin Xu,
  • Xiangmin Xu,
  • Xiangmin Xu,
  • Xiangmin Xu,
  • Chen Li,
  • Chen Li

DOI
https://doi.org/10.3389/fncir.2024.1398884
Journal volume & issue
Vol. 18

Abstract

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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.

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