FlexAlign: An Accurate and Fast Algorithm for Movie Alignment
in Cryo-Electron Microscopy

J 2020

FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy

STŘELÁK, David, Jiří FILIPOVIČ, Amaya JIMÉNEZ-MORENO, Jose María CARAZO, Carlos Óscar SÁNCHEZ SORZANO et. al.

Basic information

Original name

FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy

Authors

STŘELÁK, David (203 Czech Republic, guarantor, belonging to the institution), Jiří FILIPOVIČ (203 Czech Republic, belonging to the institution), Amaya JIMÉNEZ-MORENO, Jose María CARAZO and Carlos Óscar SÁNCHEZ SORZANO

Edition

Electronics, Switzerland, MDPI, 2020, 2079-9292

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 2.397

RIV identification code

RIV/00216224:14610/20:00116269

Organization unit

Institute of Computer Science

DOI

http://dx.doi.org/10.3390/electronics9061040

UT WoS

000551113800001

Keywords in English

cryo-em; movie alignment; acceleration; gpu; flexalign; cuda; autotuning; cufft; cufftadvisor

Abstract

V originále

Cryogenic Electron Microscopy (Cryo-EM) has been established as one of the key players in Structural Biology. It can reconstruct a 3D model of the sample at the near-atomic resolution, which led to a Method of the year award by Nature, and the Nobel Prize in 2017. With the growing number of facilities, faster microscopes, and new imaging techniques, new algorithms are needed to process the so-called movies data produced by the microscopes in real-time, while preserving a high resolution and maximum of additional information. In this article, we present a new algorithm used for movie alignment, called FlexAlign. FlexAlign is able to correctly compensate for the shift produced during the movie acquisition on-the-fly, using the current generation of hardware. The algorithm performs a global and elastic local registration of the movie frames using Cross-Correlation and B-spline interpolation for high precision. We show that our execution time is compatible with real-time correction and that we preserve the high-resolution information up to high frequency.

Links

EF16_013/0001802, research and development project

Name: CERIT Scientific Cloud

MUNI/A/1050/2019, interní kód MU

Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace IX (Acronym: SV-FI MAV IX)

Investor: Masaryk University, Category A

MUNI/A/1076/2019, interní kód MU

Name: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity 20 (Acronym: SKOMU)

Investor: Masaryk University, Category A

Citovat

STŘELÁK, David, Jiří FILIPOVIČ, Amaya JIMÉNEZ-MORENO, Jose María CARAZO and Carlos Óscar SÁNCHEZ SORZANO. FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy. Electronics. Switzerland: MDPI, 2020, vol. 9, No 6, p. 1-25. ISSN 2079-9292. Available from: https://dx.doi.org/10.3390/electronics9061040.

@article{1675418,
   author = {Střelák, David and Filipovič, Jiří and JiménezandMoreno, Amaya and Carazo, Jose María and Sánchez Sorzano, Carlos Óscar},
   article_location = {Switzerland},
   article_number = {6},
   doi = {http://dx.doi.org/10.3390/electronics9061040},
   keywords = {cryo-em; movie alignment; acceleration; gpu; flexalign; cuda; autotuning; cufft; cufftadvisor},
   language = {eng},
   issn = {2079-9292},
   journal = {Electronics},
   title = {FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy},
   url = {https://www.mdpi.com/2079-9292/9/6/1040},
   volume = {9},
   year = {2020}
}

TY  - JOUR
ID  - 1675418
AU  - Střelák, David - Filipovič, Jiří - Jiménez-Moreno, Amaya - Carazo, Jose María - Sánchez Sorzano, Carlos Óscar
PY  - 2020
TI  - FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy
JF  - Electronics
VL  - 9
IS  - 6
SP  - 1-25
EP  - 1-25
PB  - MDPI
SN  - 20799292
KW  - cryo-em
KW  - movie alignment
KW  - acceleration
KW  - gpu
KW  - flexalign
KW  - cuda
KW  - autotuning
KW  - cufft
KW  - cufftadvisor
UR  - https://www.mdpi.com/2079-9292/9/6/1040
L2  - https://www.mdpi.com/2079-9292/9/6/1040
N2  - Cryogenic Electron Microscopy (Cryo-EM) has been established as one of the key players in Structural Biology. It can reconstruct a 3D model of the sample at the near-atomic resolution, which led to a Method of the year award by Nature, and the Nobel Prize in 2017. With the growing number of facilities, faster microscopes, and new imaging techniques, new algorithms are needed to process the so-called movies data produced by the microscopes in real-time, while preserving a high resolution and maximum of additional information. In this article, we present a new algorithm used for movie alignment, called FlexAlign. FlexAlign is able to correctly compensate for the shift produced during the movie acquisition on-the-fly, using the current generation of hardware. The algorithm performs a global and elastic local registration of the movie frames using Cross-Correlation and B-spline interpolation for high precision. We show that our execution time is compatible with real-time correction and that we preserve the high-resolution information up to high frequency.
ER  -

STŘELÁK, David, Jiří FILIPOVIČ, Amaya JIMÉNEZ-MORENO, Jose María CARAZO and Carlos Óscar SÁNCHEZ SORZANO. FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy. \textit{Electronics}. Switzerland: MDPI, 2020, vol.~9, No~6, p.~1-25. ISSN~2079-9292. Available from: https://dx.doi.org/10.3390/electronics9061040.

Detailed Information on Publication Record