An image processing pipeline for electron cryo‐tomography in RELION‐5

Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three‐dimensional tomographic reconstructions, averaging images of multiple instances of...

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Published inFEBS open bio Vol. 14; no. 11; pp. 1788 - 1804
Main Authors Burt, Alister, Toader, Bogdan, Warshamanage, Rangana, Kügelgen, Andriko, Pyle, Euan, Zivanov, Jasenko, Kimanius, Dari, Bharat, Tanmay A. M., Scheres, Sjors H. W.
Format Journal Article
LanguageEnglish
Published England John Wiley & Sons, Inc 01.11.2024
John Wiley and Sons Inc
Wiley
Subjects
Automation
Bioinformatics
Cryoelectron Microscopy - methods
Electron Microscope Tomography - methods
Electron microscopes
Electron Microscopy
electron tomography
Image processing
Image Processing, Computer-Assisted - methods
Imaging, Three-Dimensional - methods
Metadata
Method
Microscopy
Models, Molecular
Open source software
Software
Structural Biology
Tomography
User interface
image processing
electron microscopy
software
electron tomography
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Abstract Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three‐dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution for de novo atomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and interoperability represents a barrier for newcomers to the field. Here, we present an image processing pipeline for electron tomography data in RELION‐5, with functionality ranging from the import of unprocessed movies to the automated building of atomic models in the final maps. Our explicit definition of metadata items that describe the steps of our pipeline has been designed for interoperability with other software tools and provides a framework for further standardisation. We present an image processing pipeline for electron cryo‐tomography data in RELION‐5 with functionality ranging from unprocessed movie import to the automated building of atomic models in final maps. The metadata describing the pipeline steps is aimed at standardisation and interoperability with other software, while the performance improvements and visual tools lead to short processing times and ease of use.
AbstractList Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three‐dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution for de novo atomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and interoperability represents a barrier for newcomers to the field. Here, we present an image processing pipeline for electron tomography data in RELION‐5, with functionality ranging from the import of unprocessed movies to the automated building of atomic models in the final maps. Our explicit definition of metadata items that describe the steps of our pipeline has been designed for interoperability with other software tools and provides a framework for further standardisation.
Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three‐dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution for de novo atomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and interoperability represents a barrier for newcomers to the field. Here, we present an image processing pipeline for electron tomography data in RELION‐5, with functionality ranging from the import of unprocessed movies to the automated building of atomic models in the final maps. Our explicit definition of metadata items that describe the steps of our pipeline has been designed for interoperability with other software tools and provides a framework for further standardisation.
Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three‐dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution for de novo atomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and interoperability represents a barrier for newcomers to the field. Here, we present an image processing pipeline for electron tomography data in RELION‐5, with functionality ranging from the import of unprocessed movies to the automated building of atomic models in the final maps. Our explicit definition of metadata items that describe the steps of our pipeline has been designed for interoperability with other software tools and provides a framework for further standardisation. We present an image processing pipeline for electron cryo‐tomography data in RELION‐5 with functionality ranging from unprocessed movie import to the automated building of atomic models in final maps. The metadata describing the pipeline steps is aimed at standardisation and interoperability with other software, while the performance improvements and visual tools lead to short processing times and ease of use.
Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three-dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution for de novo atomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and interoperability represents a barrier for newcomers to the field. Here, we present an image processing pipeline for electron tomography data in RELION-5, with functionality ranging from the import of unprocessed movies to the automated building of atomic models in the final maps. Our explicit definition of metadata items that describe the steps of our pipeline has been designed for interoperability with other software tools and provides a framework for further standardisation.Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three-dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution for de novo atomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and interoperability represents a barrier for newcomers to the field. Here, we present an image processing pipeline for electron tomography data in RELION-5, with functionality ranging from the import of unprocessed movies to the automated building of atomic models in the final maps. Our explicit definition of metadata items that describe the steps of our pipeline has been designed for interoperability with other software tools and provides a framework for further standardisation.
Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three‐dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution for de novo atomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and interoperability represents a barrier for newcomers to the field. Here, we present an image processing pipeline for electron tomography data in RELION‐5, with functionality ranging from the import of unprocessed movies to the automated building of atomic models in the final maps. Our explicit definition of metadata items that describe the steps of our pipeline has been designed for interoperability with other software tools and provides a framework for further standardisation. We present an image processing pipeline for electron cryo‐tomography data in RELION‐5 with functionality ranging from unprocessed movie import to the automated building of atomic models in final maps. The metadata describing the pipeline steps is aimed at standardisation and interoperability with other software, while the performance improvements and visual tools lead to short processing times and ease of use.
Author Toader, Bogdan
Kimanius, Dari
Zivanov, Jasenko
Warshamanage, Rangana
Scheres, Sjors H. W.
Pyle, Euan
Burt, Alister
Kügelgen, Andriko
Bharat, Tanmay A. M.
AuthorAffiliation 6 The Francis Crick Institute London UK
5 Institute of Structural and Molecular Biology, Birkbeck College London UK
3 CCP‐EM, Scientific Computing Department UKRI Science and Technology Facilities Council, Harwell Campus Didcot UK
7 Present address: European Molecular Biology Laboratory Heidelberg Germany
1 MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus Cambridge UK
2 Department of Structural Biology Genentech South San Francisco CA USA
8 Present address: CZ Imaging Institute Redwood City CA USA
4 Department of Psychiatry University of Pittsburgh Pittsburgh PA USA
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Keywords image processing
electron microscopy
software
electron tomography
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This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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Alister Burt and Bogdan Toader contributed equally to this article.
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SSID ssj0000601600
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Snippet Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided...
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StartPage 1788
SubjectTerms Automation
Bioinformatics
Cryoelectron Microscopy - methods
Electron Microscope Tomography - methods
Electron microscopes
Electron Microscopy
electron tomography
Image processing
Image Processing, Computer-Assisted - methods
Imaging, Three-Dimensional - methods
Metadata
Method
Microscopy
Models, Molecular
Open source software
Software
Structural Biology
Tomography
User interface
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Title An image processing pipeline for electron cryo‐tomography in RELION‐5
URI https://onlinelibrary.wiley.com/doi/abs/10.1002%2F2211-5463.13873
https://www.ncbi.nlm.nih.gov/pubmed/39147729
https://www.proquest.com/docview/3123657377
https://www.proquest.com/docview/3093594182
https://pubmed.ncbi.nlm.nih.gov/PMC11532982
https://doaj.org/article/5fb561fea0de49588771a1738f5ac523
Volume 14
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