Literature DB >> 34493805

Machine learning-based real-time object locator/evaluator for cryo-EM data collection.

Koji Yonekura1,2,3, Saori Maki-Yonekura4, Hisashi Naitow4, Tasuku Hamaguchi4, Kiyofumi Takaba4.   

Abstract

In cryo-electron microscopy (cryo-EM) data collection, locating a target object is error-prone. Here, we present a machine learning-based approach with a real-time object locator named yoneoLocr using YOLO, a well-known object detection system. Implementation shows its effectiveness in rapidly and precisely locating carbon holes in single particle cryo-EM and in locating crystals and evaluating electron diffraction (ED) patterns in automated cryo-electron crystallography (cryo-EX) data collection. The proposed approach will advance high-throughput and accurate data collection of images and diffraction patterns with minimal human operation.
© 2021. The Author(s).

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Year:  2021        PMID: 34493805      PMCID: PMC8423793          DOI: 10.1038/s42003-021-02577-1

Source DB:  PubMed          Journal:  Commun Biol        ISSN: 2399-3642


  21 in total

1.  Electron energy filtering significantly improves amplitude contrast of frozen-hydrated protein at 300kV.

Authors:  Koji Yonekura; Michael B Braunfeld; Saori Maki-Yonekura; David A Agard
Journal:  J Struct Biol       Date:  2006-08-15       Impact factor: 2.867

2.  Double-Helix Supramolecular Nanofibers Assembled from Negatively Curved Nanographenes.

Authors:  Kenta Kato; Kiyofumi Takaba; Saori Maki-Yonekura; Nobuhiko Mitoma; Yusuke Nakanishi; Taishi Nishihara; Taito Hatakeyama; Takuma Kawada; Yuh Hijikata; Jenny Pirillo; Lawrence T Scott; Koji Yonekura; Yasutomo Segawa; Kenichiro Itami
Journal:  J Am Chem Soc       Date:  2021-03-24       Impact factor: 15.419

3.  cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.

Authors:  Ali Punjani; John L Rubinstein; David J Fleet; Marcus A Brubaker
Journal:  Nat Methods       Date:  2017-02-06       Impact factor: 28.547

4.  Advances in cryo-EM and ED with a cold-field emission beam and energy filtration -Refinements of the CRYO ARM 300 system in RIKEN SPring-8 center.

Authors:  Saori Maki-Yonekura; Tasuku Hamaguchi; Hisashi Naitow; Kiyofumi Takaba; Koji Yonekura
Journal:  Microscopy (Oxf)       Date:  2021-03-24       Impact factor: 1.571

5.  Collecting large datasets of rotational electron diffraction with ParallEM and SerialEM.

Authors:  Kiyofumi Takaba; Saori Maki-Yonekura; Koji Yonekura
Journal:  J Struct Biol       Date:  2020-06-13       Impact factor: 2.867

6.  Real-time cryo-electron microscopy data preprocessing with Warp.

Authors:  Dimitry Tegunov; Patrick Cramer
Journal:  Nat Methods       Date:  2019-10-07       Impact factor: 28.547

7.  Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs.

Authors:  Tristan Bepler; Andrew Morin; Micah Rapp; Julia Brasch; Lawrence Shapiro; Alex J Noble; Bonnie Berger
Journal:  Nat Methods       Date:  2019-10-07       Impact factor: 28.547

8.  Topaz-Denoise: general deep denoising models for cryoEM and cryoET.

Authors:  Tristan Bepler; Kotaro Kelley; Alex J Noble; Bonnie Berger
Journal:  Nat Commun       Date:  2020-10-15       Impact factor: 14.919

9.  Protein and Organic-Molecular Crystallography With 300kV Electrons on a Direct Electron Detector.

Authors:  Kiyofumi Takaba; Saori Maki-Yonekura; Satoru Inoue; Tatsuo Hasegawa; Koji Yonekura
Journal:  Front Mol Biosci       Date:  2021-01-06

10.  Serial protein crystallography in an electron microscope.

Authors:  Robert Bücker; Pascal Hogan-Lamarre; Pedram Mehrabi; Eike C Schulz; Lindsey A Bultema; Yaroslav Gevorkov; Wolfgang Brehm; Oleksandr Yefanov; Dominik Oberthür; Günther H Kassier; R J Dwayne Miller
Journal:  Nat Commun       Date:  2020-02-21       Impact factor: 14.919

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  1 in total

1.  Automated systematic evaluation of cryo-EM specimens with SmartScope.

Authors:  Jonathan Bouvette; Qinwen Huang; Amanda A Riccio; William C Copeland; Alberto Bartesaghi; Mario J Borgnia
Journal:  Elife       Date:  2022-08-23       Impact factor: 8.713

  1 in total

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