ArticleOpen biology2021
Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography.
Article in Open biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 16 citations in OpenAlex.
- The CAHRA Challenge: A Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms.bioRxiv : the preprint server for biology · 2026Article
- CryoJAX: a cryo-electron microscopy image-simulation library in JAX.Acta crystallographica. Section D, Structural biology · 2026Article
- Electron fourier ptychography for phase reconstruction.Scientific reports · 2025Article
- cryoJAX: A Cryo-electron Microscopy Image Simulation Library In JAX.bioRxiv : the preprint server for biology · 2025Article
- Template Learning: Deep learning with domain randomization for particle picking in cryo-electron tomography.Nature communications · 2025Article
- PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modeling and machine learning.Acta crystallographica. Section F, Structural biology communications · 2025Article
- InstaMap: instant-NGP for cryo-EM density maps.Acta crystallographica. Section D, Structural biology · 2025Article
- Training Generalized Segmentation Networks with Real and Synthetic Cryo-ET data.bioRxiv : the preprint server for biology · 2025Article
- Roodmus: a toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions.IUCrJ · 2024Article
- Pillar data-acquisition strategies for cryo-electron tomography of beam-sensitive biological samples.Acta crystallographica. Section D, Structural biology · 2024Article
- Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples.Ultramicroscopy · 2024Article
- Rapid Synthesis of Cryo-ET Data for Training Deep Learning Models.bioRxiv : the preprint server for biology · 2023Article
- CryomicroscopyFaraday discussions · 2022Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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
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