ArticleNature communications2020
TranSPHIRE: automated and feedback-optimized on-the-fly processing for cryo-EM.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- An unattended image-processing pipeline for on-the-fly quality assessment and 3D exploration in cryo-EM.Acta crystallographica. Section D, Structural biology · 2026Article
- CryoEMNet driven symmetry-aware molecular reconstruction through deep learning enhanced electron microscopy.Scientific reports · 2025Article
- Few-Shot Classification of Cryo-EM Micrographs Using Triplet Loss Embeddings.bioRxiv : the preprint server for biology · 2025Article
- Article
- Multistate kinetics of the syringe-like injection mechanism of Tc toxins.Science advances · 2025Article
- Phalloidin and DNase I-bound F-actin pointed end structures reveal principles of filament stabilization and disassembly.Nature communications · 2024Article
- Structure of the human KMN complex and implications for regulation of its assembly.Nature structural & molecular biology · 2024Article
- Structure and activation mechanism of the Makes caterpillars floppy 1 toxin.Nature communications · 2023Article
- nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography.Nature methods · 2023Article
- Automated model building and protein identification in cryo-EM maps.bioRxiv : the preprint server for biology · 2023Article
- Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate.Nature communications · 2023Article
- TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining.Nature methods · 2023Article
- Design of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography.Cell reports methods · 2023Article
- MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV-visible spectroscopy combined with size-exclusion chromatography.Biophysics and physicobiology · 2023Article
- Article
- Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM.Chemical reviews · 2022Review
- Emerging Themes in CryoEM─Single Particle Analysis Image Processing.Chemical reviews · 2022Review
- Evolving Experimental Techniques for Structure-Based Drug Design.The journal of physical chemistry. B · 2022Review
- Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin.Nature communications · 2022Article
- Structure of the human inner kinetochore CCAN complex and its significance for human centromere organization.Molecular cell · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single particle cryo-EM requires full automation to allow high-throughput structure determination. Although software packages exist where parts of the cryo-EM pipeline are automated, a complete solution that offers reliable on-the-fly processing, resulting in high-resolution structures, does not exist. Here we present TranSPHIRE: A software package for fully-automated processing of cryo-EM datasets during data acquisition. TranSPHIRE transfers data from the microscope, automatically applies the common pre-processing steps, picks particles, performs 2D clustering, and 3D refinement parallel to image recording. Importantly, TranSPHIRE introduces a machine learning-based feedback loop to re-train its picking model to adapt to any given data set live during processing. This elegant approach enables TranSPHIRE to process data more effectively, producing high-quality particle stacks. TranSPHIRE collects and displays all metrics and microscope settings to allow users to quickly evaluate data during acquisition. TranSPHIRE can run on a single work station and also includes the automated processing of filaments.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.