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SciJava操作:适用于Fiji及其他领域的改进型算法框架。

SciJava Ops: an improved algorithms framework for Fiji and beyond.

作者信息

Selzer Gabriel J, Rueden Curtis T, Hiner Mark C, Evans Edward L, Kolb David, Wiedenmann Marcel, Birkhold Christian, Buchholz Tim-Oliver, Helfrich Stefan, Northan Brian, Walter Alison, Schindelin Johannes, Pietzsch Tobias, Saalfeld Stephan, Berthold Michael R, Eliceiri Kevin W

机构信息

Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States.

Morgridge Institute for Research, Madison, WI, United States.

出版信息

Front Bioinform. 2024 Sep 27;4:1435733. doi: 10.3389/fbinf.2024.1435733. eCollection 2024.

Abstract

Decades of iteration on scientific imaging hardware and software has yielded an explosion in not only the size, complexity, and heterogeneity of image datasets but also in the tooling used to analyze this data. This wealth of image analysis tools, spanning different programming languages, frameworks, and data structures, is itself a problem for data analysts who must adapt to new technologies and integrate established routines to solve increasingly complex problems. While many "bridge" layers exist to unify pairs of popular tools, there exists a need for a general solution to unify new and existing toolkits. The SciJava Ops library presented here addresses this need through two novel principles. Algorithm implementations are declared as plugins called Ops, providing a uniform interface regardless of the toolkit they came from. Users express their needs declaratively to the Op environment, which can then find and adapt available Ops on demand. By using these principles instead of direct function calls, users can write streamlined workflows while avoiding the translation boilerplate of bridge layers. Developers can easily extend SciJava Ops to introduce new libraries and more efficient, specialized algorithm implementations, even immediately benefitting existing workflows. We provide several use cases showing both user and developer benefits, as well as benchmarking data to quantify the negligible impact on overall analysis performance. We have initially deployed SciJava Ops on the Fiji platform, however it would be suitable for integration with additional analysis platforms in the future.

摘要

几十年来,科学成像硬件和软件的迭代不仅使图像数据集的规模、复杂性和异质性呈爆炸式增长,也使用于分析这些数据的工具大量涌现。如此丰富的图像分析工具,涵盖不同的编程语言、框架和数据结构,这本身就给数据分析师带来了问题,他们必须适应新技术并整合既定程序来解决日益复杂的问题。虽然存在许多“桥梁”层来统一成对的流行工具,但仍需要一种通用解决方案来统一新的和现有的工具包。这里介绍的SciJava Ops库通过两个新颖的原则满足了这一需求。算法实现被声明为称为Ops的插件,无论它们来自哪个工具包,都提供统一的接口。用户以声明方式向Op环境表达他们的需求,然后Op环境可以按需查找并适配可用的Ops。通过使用这些原则而非直接函数调用,用户可以编写简化的工作流程,同时避免桥梁层的转换样板代码。开发人员可以轻松扩展SciJava Ops以引入新库以及更高效、更专业的算法实现,甚至现有工作流程能立即从中受益。我们提供了几个用例,展示了对用户和开发人员的好处,以及基准测试数据,以量化对整体分析性能的可忽略不计的影响。我们最初在Fiji平台上部署了SciJava Ops,不过它未来适合与其他分析平台集成。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1647/11466933/57ab6d74f7ea/fbinf-04-1435733-g001.jpg

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