PFI:AIR - TT: Cost Effective Solutions for Storage and Access of Massive Imagery

这个PFI：空气技术翻译项目关注的是如何彻底改变显微镜和医疗设备的使用方式，以及它们可以回答的科学问题的潜力。当图像数据的大小不再是一个制约因素时，将微观尺度与宏观尺度联系起来的新的研究领域成为可能，例如理解视觉皮质的神经连接。通过消除使用大型图像的时间、精力和专业知识的障碍，VisStore将使科学家能够扩展他们现有的工作流程。这种能力将开启对基本生物过程、疾病的起源和发展，以及最终治疗这些疾病的药物和程序的新研究。虽然VisStore最初是为生命科学应用量身定做的，但它可以集成到显微镜中，用于新设备和新兴学科，如精密医学、材料科学和半导体。此外，VisStore有可能简化从当前工作流到完全基于云的在线工作流的过渡。此外，VisStore和分层流媒体基础设施有可能成为大体积图像的事实上的标准。这个加速创新技术转化项目将支持研发人员构建VisStore的原型，VisStore是一种即插即用设备，可以方便地存储、归档、访问、分发和处理来自显微镜或医疗设备的海量体积图像。它将研究成果转化为显微镜市场的商业应用，该市场持续增长，2014年超过41亿美元，预计复合年增长率为7.1%，而用于可靠存储、轻松访问和高效处理此类数据的所涉及的网络基础设施没有跟上步伐。这导致了可以产生的数据质量与实际使用的数据之间的差异，因为科学家不必要地限制图像大小以匹配计算能力。用于扩展到海量图像的强力解决方案价格昂贵，难以维护，而且需要的专业知识通常是较小机构无法企及的。VisStore是一种软件/硬件/云相结合的解决方案，可轻松处理任何大小的图像数据。VisStore并不比USB驱动器更复杂，它允许用户在工作组、公司甚至全球分布的环境中轻松访问、处理和分发千兆和太像素的2D和3D图像。VisStore背后的技术提高了处理海量图像的最先进水平。当数据大小超过主内存时，现代软件工具经常停止缩放，这一直是显微镜图像的限制因素。在处理图像数据时，VisStore中实施的分层流软件基础设施实质上将工作站的内存层次结构扩展到外部网络连接硬盘(NAS)，甚至是基于云的存储。由于每个组件都充当缓存，VisStore通过对专有文件布局的按需数据访问来实现性能，从而将级别之间传输的数据量降至最低，从而能够高效地扩展到任何大小的图像。这将支持以下方面的开发：(1)来自显微镜或医疗设备的图像的自动摄取和转换；(2)管理数据本地和远程存储的简单用户界面和工具；(3)选择和导出数据以与现有工作流程整合的工具。该项目邀请莫兰眼科中心、联合地区和大学病理学家公司(奥雅纳)实验室和俄勒冈健康与科学大学开发和测试获取千兆和太像素图像的原型，并测试其商业价值，将这项技术从研究发现转化为商业现实。特别是，该项目支持的研究生和本科生将直接参与这些创业活动。他们将直接与合作机构的早期技术采用者合作，并获得实践经验，了解如何识别和解决他们的痛点，并最终将原始技术转化为具有商业价值的产品。

This PFI: AIR Technology Translation project focuses on the potential to revolutionize how microscopy and medical devices are used and the science questions that they can answer. When image data size is no longer a restricting factor, new domains of study become possible relating the micro-scale to macro-scale, such as understanding the neural connectomics of the visual cortex. By removing the barrier of time, effort, and expertise to use large imagery, VisStore will enable scientists to scale their existing workflows. Such capability would open new investigations into fundamental biological processes, the origin and progression of diseases, and ultimately the drugs and procedures for curing them. Although initially tailored to life sciences applications, VisStore can be integrated in microscopy for new devices and emerging disciplines, such as precision medicine, material sciences and semiconductors. Furthermore, VisStore has the potential to ease the transition from current workflows to fully online cloud-based ones. Furthermore, VisStore and the hierarchical streaming infrastructure have the potential to become the de-facto standard for large volumetric images. This Accelerating Innovation Technology Translation project will support R&D to build a prototype of VisStore, a plug-and-play device for easy storing, archiving, accessing, distributing, and processing massive volumetric images coming from microscopy or medical devices. It translates research discovery toward commercial applications in the microscopy market which continues to grow, topping $4.1 billion in 2014 with an anticipated CAGR growth of 7.1%, while the addressed cyber-infrastructures to reliably store, easily access, and efficiently process such data have not kept pace. This has led to a discrepancy between the quality of data that could be produced, and what actually is used, as scientists unnecessarily restrict image sizes to match computational capabilities. Brute force solutions for scaling to massive images are expensive, difficult to maintain, and require expertise usually out of reach for smaller institutions. VisStore is a combined software/hardware/cloud solution that enables ease of use for image data of any size. No more complicated than a USB drive, VisStore allows users to easily access, process, and distribute giga and terapixel 2D and 3D images within a workgroup, a company, or even globally distributed environments. The technology behind VisStore enhances the state-of-the-art for handing massive image volumes. Modern software tools often stop scaling when data size exceeds main memory, and this has been a limiting factor for microscopy imagery. When dealing with image data, the hierarchical streaming software infrastructure implemented in VisStore essentially extends the memory hierarchy of a workstation to both an external network-attached hard drive (NAS), and even cloud-based storage. With each component acting as a cache, VisStore achieves performance through on-demand data access to proprietary file layout that minimizes the amount of data transferred between levels, enabling efficient scaling to images of any size. This will support development for: (i) automated ingestion and conversion of images coming from microscopy or medical devices; (ii) a simple user interface and tool to manage local and remote storage of data; and (iii) a tool to select and export data for integration with existing workflows. The project engages the Moran Eye Center, the Associated Regional and University Pathologists, Inc. (ARUP) laboratories and the Oregon Health & Science University to develop and tests a prototype acquiring giga- and teravoxel images and test its commercial value to translate this technology from research discovery towards a commercial reality. In particular, the graduate and undergraduate students supported by the project will be directly involved in these entrepreneurial activities. They will cooperate directly with the early adopters of the technology at the collaborating institutions and receive hands-on experience in how to identify and resolve their pain points and ultimately translate the raw technology into a product with commercial value.