Paper List
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Nyxus: A Next Generation Image Feature Extraction Library for the Big Data and AI Era
This paper addresses the core pain point of efficiently extracting standardized, comparable features from massive (terabyte to petabyte-scale) biomedi...
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Topological Enhancement of Protein Kinetic Stability
This work addresses the long-standing puzzle of why knotted proteins exist by demonstrating that deep knots provide a functional advantage through enh...
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A Multi-Label Temporal Convolutional Framework for Transcription Factor Binding Characterization
This paper addresses the critical limitation of existing TF binding prediction methods that treat transcription factors as independent entities, faili...
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Social Distancing Equilibria in Games under Conventional SI Dynamics
This paper solves the core problem of proving the existence and uniqueness of Nash equilibria in finite-duration SI epidemic games, showing they are a...
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Binding Free Energies without Alchemy
This paper addresses the core bottleneck of computational expense in Absolute Binding Free Energy calculations by eliminating the need for numerous al...
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SHREC: A Spectral Embedding-Based Approach for Ab-Initio Reconstruction of Helical Molecules
This paper addresses the core bottleneck in cryo-EM helical reconstruction: eliminating the dependency on accurate initial symmetry parameter estimati...
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Budget-Sensitive Discovery Scoring: A Formally Verified Framework for Evaluating AI-Guided Scientific Selection
This paper addresses the critical gap in evaluating AI-guided scientific selection strategies under realistic budget constraints, where existing metri...
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Probabilistic Joint and Individual Variation Explained (ProJIVE) for Data Integration
This paper addresses the core challenge of accurately decomposing shared (joint) and dataset-specific (individual) sources of variation in multi-modal...
使用QuPath和OMERO进行全切片和显微镜图像分析
Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
30秒速读
IN SHORT: 使QuPath能够直接分析存储在OMERO服务器中的图像而无需下载整个数据集，克服了大规模研究的本地存储限制。
核心创新
- Methodology Developed a new QuPath extension from scratch with three pixel access APIs (web, Ice, pixel data microservice) for flexible server compatibility
- Methodology Implemented unit testing with automated Docker container creation for OMERO server connections, ensuring software reliability
- Methodology Designed modular architecture separating core logic (headless operation) from GUI components, improving maintainability and scriptability
主要结论
- 自2024年2月以来，该扩展已被下载29,727次，显示了广泛的采用和活跃的用户社区。
- 支持高达20 GB未压缩的全切片图像（120,000 x 60,000像素）以及具有数十个16位/32位通道的荧光多重图像。
- 通过OMERO集成，能够访问包含超过400 TB已发布成像数据的IDR存储库。
摘要: QuPath是用于生物图像分析的开源软件。作为一个灵活且易于安装的桌面应用程序，QuPath被全球实验室用于可视化和分析大型复杂图像。然而，仅依赖存储在本地文件系统上的图像限制了QuPath在更大规模研究中的应用。本文描述了一个新的扩展，使QuPath能够从OMERO服务器访问像素和元数据。这通过允许软件高效处理远程存储的图像来增强其功能，同时也为希望将QuPath连接到其他图像管理系统的开发人员提供了模板。