TiltRec: an ultra-fast and open-source toolkit for cryo-electron tomographic reconstruction

doi:10.1093/bioinformatics/btaf068

	TiltRec: an ultra-fast and open-source toolkit for cryo-electron tomographic reconstruction
	Jiao, Yanxin 1,2; Li, Hongjia 3; Xue, Yang 1,2; Yang, Guoliang 4; Qi, Lei 5; Zhang, Fa 3; Zang, Dawei 6; Han, Renmin 1,2
	2025-03-06
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	41 期号:3 页码:5
摘要	Motivation Cryo-electron tomography (cryo-ET) has revolutionized our ability to observe structures from the subcellular to the atomic level in their native states. Achieving high-resolution reconstruction involves collecting tilt series at different angles and subsequently backprojecting them into 3D space or iteratively reconstructing them to build a 3D volume of the specimen. However, the intricate computational demands of tomographic reconstruction pose significant challenges, requiring extensive calculation times that hinder efficiency, especially with large and complex datasets.Results We present TiltRec, an open-source toolkit that leverages the parallel capabilities of Central Processing Units and Graphics Processing Units to enhance tomographic reconstruction. TiltRec implements six classical tomographic reconstruction algorithms, utilizing optimized parallel computation strategies and advanced memory management techniques. Performance evaluations across multiple datasets of varying sizes demonstrate that TiltRec significantly improves efficiency, reducing computational times while maintaining reconstruction resolution.Summary TiltRec effectively addresses the computational challenges associated with cryo-ET reconstruction by fully exploiting parallel acceleration. As an open-source tool, TiltRec not only facilitates extensive applications by the research community but also supports further algorithm modifications and extensions, enabling the continued development of novel algorithms.Availability and implementation The source code, documentation, and sample data can be downloaded at https://github.com/icthrm/TiltRec.
DOI	10.1093/bioinformatics/btaf068
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2021YFF0704300] ; Fundamental Research Funds for the Central Universities ; National Natural Science Foundation of China[62072280] ; National Natural Science Foundation of China[61932018] ; National Natural Science Foundation of China[32241027] ; National Natural Science Foundation of China[62072441] ; Natural Science Foundation of Shandong Province[ZR2023YQ057] ; Instrument Improvement Funds of Shandong University Public Technology Platform[ts20230204]
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:001438761100001
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/40727
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Zang, Dawei; Han, Renmin
作者单位	1.Shandong Univ, Qilu Hosp Qingdao, Cheeloo Coll Med, 72 Binghai Rd, Qingdao 266237, Peoples R China 2.Shandong Univ, Frontiers Sci Ctr Nonlinear Expectat, Res Ctr Math & Interdisciplinary Sci, Minist Educ, 72 Binghai Rd, Qingdao 266237, Peoples R China 3.Beijing Inst Technol, Sch Med Technol, Beijing 100081, Peoples R China 4.Jinan Ctr Dis Control & Prevent, Jinan High Tech Zone Branch Ctr, Jinan 250101, Peoples R China 5.Shandong Univ, Biomed Res Ctr Struct Anal, Jinan 250012, Peoples R China 6.Chinese Acad Sci, Inst Comp Technol, High Performance Comp Res Ctr, 6 Kexueyuan South Rd, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Jiao, Yanxin,Li, Hongjia,Xue, Yang,et al. TiltRec: an ultra-fast and open-source toolkit for cryo-electron tomographic reconstruction[J]. BIOINFORMATICS,2025,41(3):5.
APA	Jiao, Yanxin.,Li, Hongjia.,Xue, Yang.,Yang, Guoliang.,Qi, Lei.,...&Han, Renmin.(2025).TiltRec: an ultra-fast and open-source toolkit for cryo-electron tomographic reconstruction.BIOINFORMATICS,41(3),5.
MLA	Jiao, Yanxin,et al."TiltRec: an ultra-fast and open-source toolkit for cryo-electron tomographic reconstruction".BIOINFORMATICS 41.3(2025):5.