Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow
Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow
复制标题
Ot2Rec：半自动、可扩展、多软件断层扫描重建工作流程
DOI：
10.1016/j.bpj.2022.11.2482
复制
发表时间：
2023
影响因子：
3.4
通讯作者：
Bor-Yior Yee N
中科院分区：
文献类型：
--
作者：
Bor-Yior Yee N
Electron cryo-tomography (cryo-ET) is an imaging technique that produces relatively high-resolution three-dimensional images. With the advancement in microscopic and computational technologies, data collection and processing on both the hardware and software facets have become ever faster and more automated. Nowadays, tens of tilt series (up to several terabytes in total) can be collected per day, in turn shifting the experimental bottleneck to data processing. Here we present Ot2Rec, a novel workflow for performing tomographic image processing, providing access to several state-of-the-art tools within a single “wrapper” user interface. The functionality of Ot2Rec covers most tasks within a common image processing pipeline, from the motion-correction of raw multi-frame micrographs to the estimation of the true defoci from which the contrast transfer function (CTF) of images is calculated, and from the alignment of tilted image stacks to the full reconstruction of the final 3D tomogram. Moreover, Ot2Rec can carry out several novel post-processing operations such as simulation of stack point-spread functions and CTF corrections by means of deconvolution. Ot2Rec also provides automated reporting of processing parameters and quality metrics for optimisation and performance evaluation of processing workflows. Ot2Rec has been developed with the central philosophy of metadata unification. We have unified the metadata structure across the suite, so that the components within the suite can be used in a user/developer defined order (for instance, MotionCor2-> CTFFind4-> IMOD) with data flowing seamlessly between any pair of components and with consideration of required prerequisites. Lastly, Ot2Rec is an open-source program suite (Apache License V2). The raw code and documentation can be found at https://github. com/rosalindfranklininstitute/Ot2Rec.
登录
查看更多内容
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
3
作者：
Tang, Guang;Peng, Liwei;Ludtke, Steven J.
通讯作者：
Ludtke, Steven J.
玻璃化细胞的多尺度 3D 冷冻相关显微镜
DOI：
10.1101/2020.05.21.107771
发表时间：
2020
期刊：
bioRxiv
影响因子：
--
作者：
Gong;P. Mitchell;Jesús G. Galaz;Corey W. Hecksel;E. Sontag;V. Gangadharan;J. Marshman;D. Mankus;M. Bisher;Abigail K. R. Lytton;J. Frydman;K. Czymmek;W. Chiu
通讯作者：
W. Chiu
影响因子：
3
作者：
Cardone, G;Grünewald, K;Steven, AC
通讯作者：
Steven, AC
用于图像去模糊的块迭代 Richardson-Lucy 方法
影响因子：
2.4
作者：
N. Lee
通讯作者：
N. Lee