Abstract
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.
Highlights
In cryo-electron tomography, a series of projection images of a sample obtained using a transmission electron microscope (TEM) are recorded at different angles through the sample
The quality of the tomographic reconstructions in cryo-electron tomography (cryo-ET) of biological samples can vary greatly depending on the TEM instrument specifications and experimental data acquisition parameters used; a significant amount of development time is dedicated to increasing the quality and efficiency of imaging acquisition [3,4,5,6], improving data acquisition software [7], and refining data analysis and reconstruction software [8]
The microscope model is built from a set of models representing the beam, detector and objective lens, the data acquisition scheme is represented by a scan model, and the specimen is represented by a sample model
Summary
Cite this article: Parkhurst JM, Dumoux M, Basham M, Clare D, Siebert CA, Varslot T, Kirkland A, Naismith JH, Evans G. 2021 Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryoelectron tomography. Cite this article: Parkhurst JM, Dumoux M, Basham M, Clare D, Siebert CA, Varslot T, Kirkland A, Naismith JH, Evans G. 2021 Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryoelectron tomography. 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. 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. 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
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