biostudies-literatureParkhurst JMEngineering and Physical Sciences Research Council210160https://www.ebi.ac.uk/biostudies/studies/S-EPMC8548082biostudies-literatureUnknown11(10)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 <i>in silico</i> 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 convenieOpen biologyParakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography.PMC8548082EP/S025243/1Varslot TNaismith JHBasham MSiebert CAClare DParkhurst JMEvans GDumoux MKirkland AfalseParakeet: 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 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 <i>in silico</i> 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 convenie2021-01-01T00:00:00Z2021 Oct2025-05-29T22:01:38.186Z2024-11-09T08:21:49.789ZS-EPMC85480823469973210.1098/rsob.210160