{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Parkhurst JM"],"funding":["Engineering and Physical Sciences Research Council"],"pagination":["210160"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8548082"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["11(10)"],"pubmed_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 <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 convenie"],"journal":["Open biology"],"pubmed_title":["Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography."],"pmcid":["PMC8548082"],"funding_grant_id":["EP/S025243/1"],"pubmed_authors":["Varslot T","Naismith JH","Basham M","Siebert CA","Clare D","Parkhurst JM","Evans G","Dumoux M","Kirkland A"],"additional_accession":[]},"is_claimable":false,"name":"Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography.","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 <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 convenie","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Oct","modification":"2025-05-29T22:01:38.186Z","creation":"2024-11-09T08:21:49.789Z"},"accession":"S-EPMC8548082","cross_references":{"pubmed":["34699732"],"doi":["10.1098/rsob.210160"]}}