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

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格子光片显微镜(LLSM)收集的数据的获取、处理和传播。该仪器由SDSMT、南达科他大学(U.S.)和南达科他州立大学(SDSU)合作开发，为多个拟议的荧光成像研究项目做出贡献，特别是与全州生化时空网络资源(BioSNTR)合作的项目。统一的实施允许调查人员访问任何一组在线图像并将其应用于任何一组在线图像，而与数据驻留在哪里无关，也不需要在处理之前进行数据转换。LLSM的能力在于它能够捕获从广域荧光图像构建的高速三维(3-D)数据，从而在亚波长空间分辨率下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。该仪器还包括一个网络门户设计，允许地理上相距遥远的研究人员无缝访问大量荧光图像。该仪器可以进行重要的研究，有助于从根本上理解不同生物系统中的信号传递过程，并支持未来生物技术的发展，包括改进生物材料、提高对细胞信号的理解和对耐旱植物物种的了解。该仪器支持动态可视化生物系统细胞和亚细胞隔间内荧光标记标记的演变，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，并揭示利用LLSM研究的重要生物系统的结构。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开展的协作科学的纽带，具有广泛的科学、教育和社会影响。在动物和植物生物系统的细胞和亚细胞隔间内进行三维体积荧光成像的方法对于扩展当前对生命系统的理解是必要的。该仪器的推动力在于需要将初始和后续的生物图像信息学处理与LLSM仪器本身紧密结合，为研究人员提供对仪器、数据和适当处理技术的透明和无缝访问。此外，该提案强调了收集和开发这一生物图像信息学倡议所需的适当技术所需的重大努力。

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.