近日，法国波尔多大学Jean-Baptiste Sibarita及其研究组开发出显微镜的流式分析和实时工作流程Arkitekt。2024年9月18日，《自然—方法学》杂志在线发表了这项成果。

研究人员介绍了Arkitekt，这是一个开源的中介，连接用户与生物图像应用程序，实时实现复杂的定量显微镜工作流程。它允许本地或远程可靠、高效地协调流行的生物图像软件。它包括可视化和分析模块，还具有执行源代码和引导采集软件的机制，使“智能显微镜”成为现实。

据介绍，定量显微镜工作流程在过去几年中发生了显著变化，随着深度学习的出现，变得越来越复杂。

长期以来，诸如复杂显微镜数据的三维分割等挑战终于得以解决，新兴的成像模式在分辨率和采集速度上创造了记录，每天生成的数据量达到千兆字节甚至太字节。

随着生物图像工作流程的转变，对高效协调和数据管理的需求不断增加，这需要多工具互操作性以及能够跨越专用计算资源的能力。然而，现有解决方案在灵活性和可扩展性方面仍然有限，通常仅限于离线分析。

附：英文原文

Title: Arkitekt: streaming analysis and real-time workflows for microscopy

Author: Roos, Johannes, Bancelin, Stphane, Delaire, Tom, Wilhelmi, Alexander, Levet, Florian, Engelhardt, Maren, Viasnoff, Virgile, Galland, Rmi, Ngerl, U. Valentin, Sibarita, Jean-Baptiste

Issue&Volume: 2024-09-18

Abstract: Quantitative microscopy workflows have evolved dramatically over the past years, progressively becoming more complex with the emergence of deep learning. Long-standing challenges such as three-dimensional segmentation of complex microscopy data can finally be addressed, and new imaging modalities are breaking records in both resolution and acquisition speed, generating gigabytes if not terabytes of data per day. With this shift in bioimage workflows comes an increasing need for efficient orchestration and data management, necessitating multitool interoperability and the ability to span dedicated computing resources. However, existing solutions are still limited in their flexibility and scalability and are usually restricted to offline analysis. Here we introduce Arkitekt, an open-source middleman between users and bioimage apps that enables complex quantitative microscopy workflows in real time. It allows the orchestration of popular bioimage software locally or remotely in a reliable and efficient manner. It includes visualization and analysis modules, but also mechanisms to execute source code and pilot acquisition software, making ‘smart microscopy’ a reality.

DOI: 10.1038/s41592-024-02404-5

Source: https://www.nature.com/articles/s41592-024-02404-5