FluoRender: Visualization-Based and Interactive Analysis for Multichannel Microscopy Data

FluoRender：多通道显微镜数据的基于可视化和交互式分析

• 批准号: 9916753
• 负责人: Charles Hansen
• 金额: $ 34.31万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2022-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9916753
• 关键词: 3-Dimensional; Address; Architecture; Big Data; Biological; Biomedical Research; Cells; Collaborations; Complex; Computer software; Computers; Confocal Microscopy; Custom; Data; Data Analyses; Development; Embryo; Environment; Fluorescence; Fluorescence Microscopy; Goals; Image; Image Analysis; Imaging Device; International; Intuition; Investigation; Lead; Measurement; Measures; Microscopy; Modality; Modeling; Modernization; Morphology; Organelles; Organism; Research; Resolution; Sampling; Scanning; Scientist; Shapes; Signal Transduction; Speed; Standardization; Structure; Surface; System; Techniques; Three-dimensional analysis; Time; Tissues; Visualization; Work; base; biological research; cell motility; experience; fluorescence microscope; high standard; improved; insight; interactive computing; interdisciplinary collaboration; mutant; neuronal circuitry; tool; visual feedback

Summary FluoRender is a software package for visualizing and analyzing 3D and 4D (3D over time) fluorescence microscopy data. This project will serve the needs of biologists utilizing confocal microscopy for understanding cell development in many organisms and addresses the big-data problem from the massive increase of imaging data from modern high-resolution fluorescence microscopes. Specific Aim 1: Visualization of an extended number of volume channels: FluoRender will be enhanced with the multichannel visualization capability by simultaneously supporting several tens to hundreds of channels, which can be acquired from multispectral imaging devices or by registering data of multiple scans. FluoRender will take advantage of the latest volume rendering techniques to visualize significantly improved signal intensity detail compared to pseudo-surfaces. Specific Aim 2: Interactive comparison and organization of volume channels: A package of measures will be implemented in FluoRender for directly comparing volume channels. Leveraging the OpenCL programming interface, shape comparisons will be performed interactively on graphics hardware, allowing compound measures for complex morphology as well as immediate visual feedback via multichannel visualization. Interactive comparison will further enable the development of functions for semiautomatic channel organization and multichannel colocalization analysis. Specific Aim 3: 4D tracking of structures with irregular and changing shapes: Tracking irregularly shaped and shape-changing structures will substantially expand FluoRender's application for developmental and morphological studies of intracellular organelles, cells, and tissues. This will include a comprehensive tracking system that integrates different modules and allows them to work in an iterative and integrated environment, allowing user-guided, progressive refinement of the segmentation and tracking results. Specific Aim 4. Fully hardware-accelerated and customizable computing modules: FluoRender will be restructures using compute modules based on the OpenCL standard, which provides not only hardware-accelerated execution speed, but also convenience for customization and reuse. Computing modules will be integrated with visualization features, enabling interactive and visualization-centered analysis. Users will also be able to reorganize and build modules to customize specific workflows for great adaptability.

概括 FluoRender 是一个用于可视化和分析 3D 和 4D（随时间变化的 3D）的软件包 荧光显微镜数据。该项目将满足生物学家利用共聚焦的需求 显微镜用于了解许多生物体的细胞发育并解决大数据问题 现代高分辨率荧光成像数据大量增加带来的问题 显微镜。具体目标 1：扩展数量通道的可视化： FluoRender 将通过同时增强多通道可视化功能 支持数十至数百个通道，可从多光谱获取 成像设备或通过注册多次扫描的数据。 FluoRender 将利用 最新的体积渲染技术可显着改善信号强度细节 与伪表面相比。具体目标 2：交互式比较和组织 音量通道：FluoRender 中将实施一揽子措施，以直接 比较音量通道。利用 OpenCL 编程接口，形状比较 将在图形硬件上交互式执行，允许对复杂的情况进行复合测量 形态以及通过多通道可视化的即时视觉反馈。交互的 比较将进一步促进半自动通道功能的开发 组织和多渠道共定位分析。具体目标 3：结构的 4D 跟踪 具有不规则和变化的形状：跟踪不规则形状和形状变化 结构将大大扩展 FluoRender 的应用，用于开发和 细胞内细胞器、细胞和组织的形态学研究。这将包括一个 综合跟踪系统，集成了不同的模块并允许它们在一个 迭代和集成环境，允许用户引导、逐步完善 分割和跟踪结果。具体目标 4. 完全硬件加速和 可定制的计算模块：FluoRender将使用计算模块进行重组 基于OpenCL标准，不仅提供硬件加速的执行速度， 而且还方便定制和重用。计算模块将集成 可视化功能，实现交互式和以可视化为中心的分析。用户还将 能够重新组织和构建模块来定制特定的工作流程，具有很强的适应性。