ArticleJournal of structural biology2012
Automated tracing of filaments in 3D electron tomography reconstructions using Sculptor and Situs.
Article in Journal of structural biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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
29 citing papers in PubMed, 1 synthesis or guideline pooled it.
- 3D Segmentation Algorithms for Computerized Tomographic Imaging: a Systematic Literature Review.Journal of digital imaging · 2018Pooled it
- Article
- ModeHunter: A Package for the Reductionist Analysis, Animation, and Application of Elastic Biomolecular Motion.The journal of physical chemistry. B · 2025Article
- Evaluating Deep Learning Architectures for Actin Filament Segmentation under Varying Noise Conditions in Simulated Cryo-ET Tomograms.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2025Article
- DUAL: deep unsupervised simultaneous simulation and denoising for cryo-electron tomography.bioRxiv : the preprint server for biology · 2024Article
- Untangling Irregular Actin Cytoskeleton Architectures in Tomograms of the Cell withInternational journal of molecular sciences · 2023Article
- Computational Methods Toward Unbiased Pattern Mining and Structure Determination in Cryo-Electron Tomography Data.Journal of molecular biology · 2023Review
- In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview.Sub-cellular biochemistry · 2023Review
- Tracing Randomly Oriented Filaments in a Simulated Actin Network Tomogram.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2022Article
- Spaghetti Tracer: A Framework for Tracing Semiregular Filamentous Densities in 3D Tomograms.Biomolecules · 2022Article
- Article
- Tracing Filaments in Simulated 3D Cryo-Electron Tomography Maps Using a Fast Dynamic Programming Algorithm.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2021Article
- Cryo-electron tomography provides topological insights into mutant huntingtin exon 1 and polyQ aggregates.Communications biology · 2021Article
- QUANTIFYING ACTIN FILAMENTS IN MICROSCOPIC IMAGES USING KEYPOINT DETECTION TECHNIQUES AND A FAST MARCHING ALGORITHM.Proceedings. International Conference on Image Processing · 2020Article
- Correction of Missing-Wedge Artifacts in Filamentous Tomograms by Template-Based Constrained Deconvolution.Journal of chemical information and modeling · 2020Article
- Tracing Actin Filament Bundles in Three-Dimensional Electron Tomography Density Maps of Hair Cell Stereocilia.Molecules (Basel, Switzerland) · 2018Article
- Volume Segmentation and Analysis of Biological Materials Using SuRVoS (Super-region Volume Segmentation) Workbench.Journal of visualized experiments : JoVE · 2017Article
- Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- Constrained Cyclic Coordinate Descent for Cryo-EM Images at Medium Resolutions: Beyond the Protein Loop Closure Problem.Robotica · 2016Article
- A Robust Actin Filaments Image Analysis Framework.PLoS computational biology · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The molecular graphics program Sculptor and the command-line suite Situs are software packages for the integration of biophysical data across spatial resolution scales. Herein, we provide an overview of recently developed tools relevant to cryo-electron tomography (cryo-ET), with an emphasis on functionality supported by Situs 2.7.1 and Sculptor 2.1.1. We describe a work flow for automatically segmenting filaments in cryo-ET maps including denoising, local normalization, feature detection, and tracing. Tomograms of cellular actin networks exhibit both cross-linked and bundled filament densities. Such filamentous regions in cryo-ET data sets can then be segmented using a stochastic template-based search, VolTrac. The approach combines a genetic algorithm and a bidirectional expansion with a tabu search strategy to localize and characterize filamentous regions. The automated filament segmentation by VolTrac compares well to a manual one performed by expert users, and it allows an efficient and reproducible analysis of large data sets. The software is free, open source, and can be used on Linux, Macintosh or Windows computers.
Indexed as
Identifiers
What OpenQuestion holds
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.