Yee Neville B-Y, Ho Elaine M L, Tun Win, Smith Jake L R, Dumoux Maud, Grange Michael, Darrow Michele C, Basham Mark
Artificial Intelligence and Informatics, Rosalind Franklin Institute, Didcot, United Kingdom.
Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
Biol Imaging. 2023 Mar 29;3:e10. doi: 10.1017/S2633903X23000107. eCollection 2023.
Electron cryo-tomography is an imaging technique for probing 3D structures with at the nanometer scale. This technique has been used extensively in the biomedical field to study the complex structures of proteins and other macromolecules. With the advancement in technology, microscopes are currently capable of producing images amounting to terabytes of data per day, posing great challenges for scientists as the speed of processing of the images cannot keep up with the ever-higher throughput of the microscopes. Therefore, automation is an essential and natural pathway on which image processing-from individual micrographs to full tomograms-is developing. In this paper, we present Ot2Rec, an open-source pipelining tool which aims to enable scientists to build their own processing workflows in a flexible and automatic manner. The basic building blocks of Ot2Rec are plugins which follow a unified application programming interface structure, making it simple for scientists to contribute to Ot2Rec by adding features which are not already available. In this paper, we also present three case studies of image processing using Ot2Rec, through which we demonstrate the speedup of using a semi-automatic workflow over a manual one, the possibility of writing and using custom (prototype) plugins, and the flexibility of Ot2Rec which enables the mix-and-match of plugins. We also demonstrate, in the Supplementary Material, a built-in reporting feature in Ot2Rec which aggregates the metadata from all process being run, and output them in the Jupyter Notebook and/or HTML formats for quick review of image processing quality. Ot2Rec can be found at https://github.com/rosalindfranklininstitute/ot2rec.
电子冷冻断层扫描是一种用于探测纳米级三维结构的成像技术。该技术已在生物医学领域广泛应用于研究蛋白质和其他大分子的复杂结构。随着技术的进步，显微镜目前每天能够生成多达数TB的数据图像，这给科学家带来了巨大挑战，因为图像处理速度跟不上显微镜不断提高的通量。因此，自动化是图像处理（从单个显微图像到完整断层图像）发展的一条必不可少且自然的途径。在本文中，我们介绍了Ot2Rec，这是一个开源的流水线工具，旨在使科学家能够以灵活且自动的方式构建自己的处理工作流程。Ot2Rec的基本构建块是插件，这些插件遵循统一的应用程序编程接口结构，这使得科学家通过添加尚未具备的功能为Ot2Rec做出贡献变得很简单。在本文中，我们还展示了使用Ot2Rec进行图像处理的三个案例研究，通过这些案例我们展示了使用半自动工作流程比手动工作流程的加速效果、编写和使用自定义（原型）插件的可能性以及Ot2Rec能够实现插件混合搭配的灵活性。我们还在补充材料中展示了Ot2Rec的一个内置报告功能，该功能汇总正在运行的所有过程的元数据，并以Jupyter Notebook和/或HTML格式输出，以便快速查看图像处理质量。Ot2Rec可在https://github.com/rosalindfranklininstitute/ot2rec上获取。
