Continuous development of nTracer2 and its deployment at NIH image repositories

nTracer2 的持续开发及其在 NIH 图像存储库中的部署

基本信息

批准号：
10726178
负责人：
Dawen Cai
金额：
$ 251.57万
依托单位：
UNIVERSITY OF MICHIGAN AT ANN ARBOR
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-08-07 至 2026-08-06
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10726178
关键词：
Adoption Anatomy BRAIN initiative Blood Vessels Brain Brain imaging Cell Nucleus Cell model Cells Cellular Phone Cellular Structures Collaborations Communities Computer Systems Computer software Computers Data Data Science Data Set Databases Degenerative Disorder Deposition Development Documentation Ecosystem Educational workshop Funding General Population Group Meetings High Performance Computing Home Image Individual Internet Label Location Metadata Methodology Methods Microscopy Modality Modernization Modification Molecular Morphology Mus Neurons Neurosciences Neurosciences Research Performance Privatization Publishing Research Research Personnel Resolution Resources Series Services Slice Software Engineering Source Standardization Synapses Tissues United States National Institutes of Health Visualization Work cell type cloud based computing resources data access data format data framework data handling data management data repository data resource data sharing data standards data submission developmental disease file format fluorescence imaging hackathon high throughput screening image archival system image visualization improved indexing machine vision multimodal data multimodality neural neuroinformatics neuronal cell body novel public repository reconstruction repository response software development supercomputer technology research and development terabyte testing access tool transcriptomics usability web portal working group

项目摘要

Abstract In response to the BRAIN Initiative “Integration and Analysis of BRAIN Initiative Data” FOA, we propose further developing nTracer2, a cloud-based platform for brain image visualization and neuron tracing in the web browser. To evaluate nTracer2’s real-world performance, we deployed nTracer2 at the NIH Brain Image Library (BIL) at the Pittsburgh Supercomputer Center to handle whole mouse brain fMOST fluorescence image datasets. In a public data access test, up to 50 users across the globe smoothly explored this dataset simultaneously. In this project, our team will work on four Aims. In Aim 1, we will establish our novel SISF data framework as a scalable image data standard, which includes creating better data format conversion tools, compression filters, and documentation for SISF. In Aim 2, we will continue to develop the nTracer2 (content delivery network) CDN server, which includes upgrading the data management interface and optimizing the performance of the reconstruction database. In Aim 3, we will continue to develop the nTracer2 application server, which includes developing user management tools, optimizing high-performance computing performance for existing brain registration and machine vision functions, integrating imaging datasets taken by multimodal microscopy modalities, and expanding its neuroinformatics functions. In Aim 4, we will deploy full-stack nTracer2 at BIL and integrate CCF-registered multimodal datasets stored at multiple NIH repositories.

抽象的为了响应 BRAIN Initiative“BRAIN Initiative 数据整合与分析”FOA，我们建议进一步开发 nTracer2，这是一个基于云的平台，用于大脑图像可视化和神经元追踪为了评估 nTracer2 的实际性能，我们在 NIH 部署了 nTracer2。匹兹堡超级计算机中心的大脑图像库 (BIL) 可处理整个小鼠大脑 fMOST 在公开数据访问测试中，全球多达 50 个用户顺利访问。在这个项目中，我们的团队将同时探索这个数据集，在目标 1 中，我们将致力于实现四个目标。建立我们新颖的 SISF 数据框架作为可扩展的图像数据标准，其中包括创建在目标 2 中，我们将提供更好的数据格式转换工具、压缩过滤器和 SISF 文档。继续开发nTracer2（内容分发网络）CDN服务器，其中包括升级在目标3中，数据管理界面和优化重建数据库的性能。我们将继续开发nTracer2应用服务器，其中包括开发用户管理工具，优化现有大脑注册的高性能计算性能和机器视觉功能，集成多模态显微镜模式拍摄的成像数据集，及其神经信息学扩展功能在目标 4 中，我们将在 BIL 和 BIL 部署全栈 nTracer2。集成存储在多个 NIH 存储库中的 CCF 注册多模式数据集。