ArticleJournal of structural biology2022
ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation.
Article in Journal of structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed.
- MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography.Nature methods · 2026Article
- CoCryoViS: Collaborative online cryo-electron tomography visualization system.Protein science : a publication of the Protein Society · 2026Article
- FlyTomo: a streamlined software for on-the-fly cryo-ET data processing and diagnosis.Nature communications · 2026Article
- AreTomoLive: automated reconstruction of comprehensively corrected and denoised cryo-electron tomograms in real time and at high throughput.Nature methods · 2026Article
- Structural Analysis of Membrane Proteins in Cell-Derived Microvesicles.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries.Current opinion in structural biology · 2025Review
- A case for community metadata standards in cryo-electron tomography.Emerging topics in life sciences · 2025Review
- Methods to Study Poxvirus Structures by Cryo-EM Imaging Modalities.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- An image processing pipeline for electron cryo-tomography in RELION-5.FEBS open bio · 2024Article
- TOMOMAN: a software package for large scale cryo-electron tomography data preprocessing, community data sharing, and collaborative computing.bioRxiv : the preprint server for biology · 2024Article
- CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells.Nature methods · 2024Article
- Advances in cryo-ET data processing: meeting the demands of visual proteomics.Current opinion in structural biology · 2024Review
- TomoNet: A streamlined cryogenic electron tomography software pipeline with automatic particle picking on flexible lattices.Biological imaging · 2024Article
- The advent of preventive high-resolution structural histopathology by artificial-intelligence-powered cryogenic electron tomography.Frontiers in molecular biosciences · 2024Review
- 3D Cryo-Correlative Methods to Study Virus Structure and Dynamics Within Cells.Sub-cellular biochemistry · 2024Review
- MDSPACE and MDTOMO Software for Extracting Continuous Conformational Landscapes from Datasets of Single Particle Images and Subtomograms Based on Molecular Dynamics Simulations: Latest Developments in ContinuousFlex Software Package.International journal of molecular sciences · 2023Article
- Cryo-EM of a heterogeneous biochemical fraction elucidates multiple protein complexes from a multicellular thermophilic eukaryote.Journal of structural biology: X · 2023Article
- Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR.Nature communications · 2023Article
- Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM.Acta crystallographica. Section D, Structural biology · 2023Article
Corrections and comments
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Authors and funding
30 authors.
Funding
Abstract
Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) in cryogenic electron microscopy (cryoEM) was a few years ago. Its data processing workflows are far from being well defined and the user experience is still not smooth. Moreover, file formats of different software packages and their associated metadata are not standardized, mainly since different packages are developed by different groups, focusing on different steps of the data processing pipeline. The Scipion framework, originally developed for SPA (de la Rosa-Trevín et al., 2016), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (Martínez et al., 2020). In this article, we provide an extension of Scipion based on a set of tomography plugins (referred to as ScipionTomo hereafter), with a similar purpose: to allow users to be focused on the data processing and analysis instead of having to deal with multiple software installation issues and the inconvenience of switching from one to another, converting metadata files, managing possible incompatibilities, scripting (writing a simple program in a language that the computer must convert to machine language each time the program is run), etcetera. Additionally, having all the software available in an integrated platform allows comparing the results of different algorithms trying to solve the same problem. In this way, the commonalities and differences between estimated parameters shed light on which results can be more trusted than others. ScipionTomo is developed by a collaborative multidisciplinary team composed of Scipion team engineers, structural biologists, and in some cases, the developers whose software packages have been integrated. It is open to anyone in the field willing to contribute to this project. The result is a framework extension that combines the acquired knowledge of Scipion developers in close collaboration with third-party developers, and the on-demand design of functionalities requested by beta testers applying this solution to actual biological problems.
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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.