Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography
In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a ‘digital twin’ software pipeline for the assessme...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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The Royal Society
2021-10-01
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| Series: | Open Biology |
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| Online Access: | https://royalsocietypublishing.org/doi/10.1098/rsob.210160 |
| _version_ | 1827906481624711168 |
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| author | James M. Parkhurst Maud Dumoux Mark Basham Daniel Clare C. Alistair Siebert Trond Varslot Angus Kirkland James H. Naismith Gwyndaf Evans |
| author_facet | James M. Parkhurst Maud Dumoux Mark Basham Daniel Clare C. Alistair Siebert Trond Varslot Angus Kirkland James H. Naismith Gwyndaf Evans |
| author_sort | James M. Parkhurst |
| collection | DOAJ |
| description | In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a ‘digital twin’ software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured. |
| first_indexed | 2024-03-13T00:57:08Z |
| format | Article |
| id | doaj.art-70cf5223a322452fb78cf19561387825 |
| institution | Directory Open Access Journal |
| issn | 2046-2441 |
| language | English |
| last_indexed | 2024-03-13T00:57:08Z |
| publishDate | 2021-10-01 |
| publisher | The Royal Society |
| record_format | Article |
| series | Open Biology |
| spelling | doaj.art-70cf5223a322452fb78cf195613878252023-07-06T16:15:24ZengThe Royal SocietyOpen Biology2046-24412021-10-01111010.1098/rsob.210160Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomographyJames M. Parkhurst0Maud Dumoux1Mark Basham2Daniel Clare3C. Alistair Siebert4Trond Varslot5Angus Kirkland6James H. Naismith7Gwyndaf Evans8Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UKRosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UKRosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UKDiamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UKDiamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UKThermo Fisher Scientific, Vlastimila Pecha, Brno, Czech RepublicRosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UKRosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UKRosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UKIn cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a ‘digital twin’ software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured.https://royalsocietypublishing.org/doi/10.1098/rsob.210160digital twinelectron microscopytomographymultislice simulation |
| spellingShingle | James M. Parkhurst Maud Dumoux Mark Basham Daniel Clare C. Alistair Siebert Trond Varslot Angus Kirkland James H. Naismith Gwyndaf Evans Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography Open Biology digital twin electron microscopy tomography multislice simulation |
| title | Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography |
| title_full | Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography |
| title_fullStr | Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography |
| title_full_unstemmed | Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography |
| title_short | Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography |
| title_sort | parakeet a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo electron tomography |
| topic | digital twin electron microscopy tomography multislice simulation |
| url | https://royalsocietypublishing.org/doi/10.1098/rsob.210160 |
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