Frontiers | Brain image data processing using collaborative data workflows on Texera

IF 3.4 3区医学 Q2 NEUROSCIENCES

Frontiers in Neural Circuits Pub Date : 2024-06-20 DOI:10.3389/fncir.2024.1398884

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

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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.

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前沿｜利用 Texera 上的协作数据工作流处理脑图像数据

在神经科学领域，绘制大脑的三维（3D）神经回路和结构图对于加深我们对神经回路组织和功能的理解非常重要。本研究提出了一种新颖的方法，利用名为 "Texera "的协作数据分析平台将小鼠大脑样本转化为详细的三维大脑模型。用户友好的 Texera 平台允许神经科学、计算机视觉和数据处理团队成员之间进行有效的跨学科合作。我们的管道利用串行双光子断层扫描/TissueCyte 系统的瓦片图像，然后将瓦片图像缝合到脑切片图像中，并构建三维全脑图像数据集。生成的三维数据支持下游分析，包括三维全脑配准、基于图谱的分割、细胞计数和高分辨率容积可视化。利用这一平台，我们采用了专门的优化方法，显著提高了工作流程操作的性能。我们希望神经科学界能采用我们的方法进行基于图像的大规模数据处理和分析。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Frontiers in Neural Circuits NEUROSCIENCES-

CiteScore

6.00

自引率

5.70%

发文量

135

审稿时长

4-8 weeks

期刊介绍： Frontiers in Neural Circuits publishes rigorously peer-reviewed research on the emergent properties of neural circuits - the elementary modules of the brain. Specialty Chief Editors Takao K. Hensch and Edward Ruthazer at Harvard University and McGill University respectively, are supported by an outstanding Editorial Board of international experts. This multidisciplinary open-access journal is at the forefront of disseminating and communicating scientific knowledge and impactful discoveries to researchers, academics and the public worldwide. Frontiers in Neural Circuits launched in 2011 with great success and remains a "central watering hole" for research in neural circuits, serving the community worldwide to share data, ideas and inspiration. Articles revealing the anatomy, physiology, development or function of any neural circuitry in any species (from sponges to humans) are welcome. Our common thread seeks the computational strategies used by different circuits to link their structure with function (perceptual, motor, or internal), the general rules by which they operate, and how their particular designs lead to the emergence of complex properties and behaviors. Submissions focused on synaptic, cellular and connectivity principles in neural microcircuits using multidisciplinary approaches, especially newer molecular, developmental and genetic tools, are encouraged. Studies with an evolutionary perspective to better understand how circuit design and capabilities evolved to produce progressively more complex properties and behaviors are especially welcome. The journal is further interested in research revealing how plasticity shapes the structural and functional architecture of neural circuits.