4.6 Article

Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography

期刊

OPEN BIOLOGY
卷 11, 期 10, 页码 -

出版社

ROYAL SOC
DOI: 10.1098/rsob.210160

关键词

digital twin; electron microscopy; tomography; multislice simulation

资金

  1. Wellcome Trust through the Electrifying Life Science grant
  2. EPSRC

向作者/读者索取更多资源

Parakeet is a digital twin software for assessing the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions, and optimizing the performance and utilization of physical instruments for in silico optimization of sample geometries, data acquisition schemes, and instrument parameters.
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 degrees tilt range might be measured.

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