MRI: Development of a Scalable High Performance Computing System in Support of the Lattice Light-sheet Microscope for Real-time Three-dimensional Imaging of Living Cells

MRI：开发可扩展的高性能计算系统，支持晶格光片显微镜对活细胞进行实时三维成像

• 批准号: 1626579
• 负责人: Robert Anderson
• 金额: $ 30万
• 依托单位: South Dakota School of Mines and Technology
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-10-01 至 2022-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1626579&HistoricalAwards=false
• 关键词: MRI; Development; Scalable; Performance; Computing

This project, developing a scalable high performance computational system, aims to support the acquisition, processing, and dissemination of data collected by the recently constructed Lattice Light-Sheet Microscope (LLSM). Developed in collaboration between SDSMT, the University of South Dakota (USD), and South Dakota State University (SDSU), the instrument contributes to multiple proposed fluorescence imaging research projects, especially those in conjunction with the statewide Biochemical Spatiotemporal NeTwork Resource (BioSNTR) collaboration. The unified implementation allows investigators to access and apply any set of algorithms to any set of on-line imagery, independent of where the data resides and without requiring data conversion before processing. The power of the LLSM lies in its ability to capture high-speed three-dimensional (3-D) data constructed from wide-field fluorescence images, resulting in real-time volumetric imaging of living cells at sub-wavelength spatial resolution. To effectively utilize the capabilities of this advanced microscopy technique, significant computational hardware and software solutions must be developed to address the specific needs of this ultra-wide bandwidth system. The instrumentation also includes a web-portal design to allow geographically distant researchers seamless access to large volumes of fluorescence imagery. The instrumentation enables important studies that could contribute to the fundamental understanding of signaling processes in diverse biological systems and support the development of future bio-technologies, including improved bio-materials, improved understanding of cell signaling, and improved understanding of drought-tolerant plant species.The instrumentation supports the need to dynamically visualize the evolution of fluorescently labeled markers within cellular and sub-cellular compartments of biological systems to inform bioinformatics studies and systems biology approaches towards the understanding and discovery of regulatory networks in biological systems, and to reveal the architecture of important biological systems studied with the LLSM. This project serves as the nexus for collaborative science undertaken by a diverse group of physicists, computer scientists, biologists, and chemical engineers with broad scientific, educational, and societal impacts. Methods for 3-D volumetric fluorescence imaging within cellular and sub-cellular compartments of animal and plant biological systems are necessary to extend current understanding of living systems. The impetus for the instrument resides in the need to tightly couple initial and subsequent bioimage informatics processing with the LLSM instrument itself, providing investigators with transparent and seamless access to the instrument, data, and appropriate processing techniques. Furthermore, the proposal emphasizes the significant effort needed to both collect and develop the appropriate techniques needed for this bioimage informatics initiative.

该项目开发了一个可扩展的高性能计算系统，旨在支持最近建造的点阵光片显微镜（LLSM）收集的数据的采集，处理和传播。 SDSMT、南达科他州大学（USD）和南达科他州州立大学（SDSU）合作开发，该仪器有助于多个拟议的荧光成像研究项目，特别是与全州生物化学时空网络资源（BioSNTR）合作的项目。统一的实施使调查人员能够访问和应用任何一套算法的任何一套在线图像，独立的数据驻留在哪里，而不需要数据转换前处理。LLSM的强大之处在于它能够捕获从宽场荧光图像构建的高速三维（3-D）数据，从而以亚波长空间分辨率对活细胞进行实时体积成像。为了有效地利用这种先进的显微镜技术的能力，必须开发重要的计算硬件和软件解决方案，以满足这种超宽带系统的特定需求。该仪器还包括一个门户网站设计，允许地理上遥远的研究人员无缝访问大量的荧光图像。该仪器能够进行重要的研究，有助于对不同生物系统中信号传导过程的基本理解，并支持未来生物技术的发展，包括改进生物材料，提高对细胞信号传导的理解，该仪器支持动态可视化细胞和亚细胞内荧光标记物进化的需要。生物系统的细胞区室，为生物信息学研究和系统生物学方法提供信息，以了解和发现生物系统中的调控网络，并揭示使用LLSM研究的重要生物系统的架构。该项目是由物理学家，计算机科学家，生物学家和化学工程师组成的不同群体进行的协作科学的纽带，具有广泛的科学，教育和社会影响。动物和植物生物系统的细胞和亚细胞区室内的3-D体积荧光成像方法对于扩展当前对生命系统的理解是必要的。该仪器的动力在于需要将初始和后续的生物图像信息学处理与LLSM仪器本身紧密耦合，为研究人员提供透明和无缝的仪器，数据和适当的处理技术。此外，该提案强调了为收集和开发这一生物图像信息学举措所需的适当技术所需的重大努力。