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Tools and Technologies for Visualizing Multi-Scale Data


Fast-Track proposals will be accepted. Direct-to-Phase II proposals will NOT be accepted. Number of anticipated awards: 3-5 Budget (total costs, per award): Phase I: up to $400,000 for up to 9 months Phase II: up to $2,000,000 for up to 2 years PROPOSALS THAT EXCEED THE BUDGET OR PROJECT DURATION LISTED ABOVE MAY NOT BE FUNDED. Summary Emerging single-cell and in situ technologies are facilitating the characterization of normal, diseased, stromal, and immune cells in human tissues. Coupling these data with imaging modalities that provide information about tissue composition, gross organ structure, and metabolism while incorporating longitudinal clinical data can improve our understanding of the development and evolution of disease. Several recent initiatives have focused on generating ‘atlases’ that integrate multi- scale maps to facilitate our understanding of health and disease. These include the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative, the Human BioMolecular Atlas Program (HuBMAP), the Human Cell Atlas (HCA) initiative, and the Human Tumor Atlas Network (HTAN). Additionally, the rapid advancement of single-cell genomic- and imaging-based technologies has expanded the use of these tools in individual research projects supported by the NIH and NCI. Spatial atlas mapping efforts seek to analyze and integrate multi-scale and multi-modal data sets to generate cohesive multi- dimensional maps of normal and diseased tissues and provide them in a user-friendly environment for the research and clinical communities. Tumor atlases may include single-cell resolution data describing the tumor itself, the tumor microenvironment, and the immune milieu. A major challenge to realizing the full potential of tumor atlases is the lack of tools for the visualization of data across scales and modalities. The purpose of this contract topic is to incentivize small businesses to develop technologies that allow integrative multi-scale data visualization to facilitate building and sharing of atlases. Project Goals The goal of this project is to promote integrative visualization of multi-scale data. Potential tools or technologies would include, but are not limited to: • Web-based or containerized visualization tools that allow seamless traversal across scales of heterogenous or integrated datasets from genetic to molecular to cellular to tissue scales • Virtual Reality / Augmented Reality systems that let users interact with and manipulate multi-scale data in novel ways, using efficient interaction paradigms • Visualization tools and methods for intuitive display of high-dimensional multi-scale data and metadata in context, such as integration of cell and tissue image data with accessible genomic profile information • Visualization tools and methods that display and / or capture the heterogenous quality, uncertainty, or provenance of integrated data sets • Tools that combine existing visualization sources to facilitate and construct multi-scale visualizations For this project, data scales are defined as: 1. Genomic (e.g., DNA sequence, epigenetic state) 2. Molecular/subcellular (e.g., RNA abundance, protein abundance, intracellular structures) 3. Cellular (e.g., cell-state, cell-type) 4. Tissue (e.g., tissue morphology, histology, metabolic state) 5. Individual patient (e.g., clinical data, exposure, microbiome) 6. Population (e.g., epidemiological) Activities not responsive to announcement: Work that would not fall under this topic include: (1) approaches for visualization at a single scale and (2) approaches that focus on analysis and do not include data visualization as the major component. Phase I Activities and Deliverables: The goal of Phase I is to develop proof-of-concept or prototype tools, technologies, or products for visualizing multi-scale biomedical data. Activities and deliverables include: • Identify and define at least three scales of data (as defined above) that will be part of the Phase I visualization tool. • Identify relevant use cases for the proposed tool. • Identify one or more user communities this visualization tool will support. Communities include: (1) basic researchers, (2) computational researcher, (3) clinicians / clinical researchers, and (4) the public. • Identify and justify development of a tool or technology for visualization of multi-scale data, including the rationale for the selection of data scales and user communities. • Describe the current state of the art technologies, if any, for visualizing the selected data scales. • Develop a minimal viable product for visualizing multi-scale data capable of ingesting and visualizing the relevant data types. • Carryout initial alpha-testing by the appropriate user communities to solicit user feedback. • Specify and justify quantitative milestones that can be used to evaluate the success of the tool or technology being developed. Phase II Activities and Deliverables: The goal of Phase II is an optimized commercial tool or technology for visualizing multi-scale biomedical data. Deliverables and activities include: • Revise the minimal viable product based on user feedback to add features or functionalities and increase the use- ability and stability of the tool or technology. • Expand the tool or technology to support the integrative multi-scale visualization of at least four scales of data defined above. • Make the tool or technology compatible with a wide-range of web browsers and / or operating systems as applicable. • Carryout beta-testing by the appropriate user communities to solicit additional user feedback. • Further revise the visualization tool or technology based on user feedback focusing on the transitions between data scales and preserving the relationship of data across scales. • Develop SOPs and user documentation.
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