ArticleScientific reports2015
SOAX: a software for quantification of 3D biopolymer networks.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
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- GraFT: A robust network-based spatiotemporal analysis of filamentous structures.Science advances · 2026Article
- NEK7 phosphorylation of cortactin modulates the migratory capacity of cells expressing EML4-ALK V3.Scientific reports · 2026Article
- From Pixels to Patterns: A Multidimensional Framework to Decode Cytoskeletal Organization.Computational and structural biotechnology journal · 2026Review
- Three-dimensional robotic structures fabricated and powered entirely with proteins.Nature protocols · 2026Review
- BlinkFusion: modular platform quantifying labeling efficiency and photophysics in regular and super-resolution fluorescence microscopy.Frontiers in bioinformatics · 2026Article
- A novel computational approach to dissect the cytoskeletal architecture of cancer cells with invasive potential.Scientific reports · 2025Article
- Global alignment and local curvature of microtubules in mouse fibroblasts are robust against perturbations of vimentin and actin.Soft matter · 2025Article
- Active membrane deformations of a minimal synthetic cell.Nature physics · 2025Article
- KnotResolver: tracking self-intersecting filaments in microscopy using directed graphs.Bioinformatics (Oxford, England) · 2024Article
- Data-Driven and Cell-Specific Determination of Nuclei-Associated Actin Structure.Small structures · 2024Article
- Design and Construction of a Multi-Tiered Minimal Actin Cortex for Structural Support in Lipid Bilayer Applications.ACS applied bio materials · 2024Article
- Collagen fiber centerline tracking in fibrotic tissue via deep neural networks with variational autoencoder-based synthetic training data generation.Medical image analysis · 2023Article
- Dynamic remodeling of actin networks by cyclase-associated protein and CAP-Abp1 complexes.Current biology : CB · 2023Article
- Automatic extraction of actin networks in plants.PLoS computational biology · 2023Article
- Data driven and cell specific determination of nuclei-associated actin structure.bioRxiv : the preprint server for biology · 2023Article
- Extracellular Cues Govern Shape and Cytoskeletal Organization in Giant Unilamellar Lipid Vesicles.ACS synthetic biology · 2023Article
- Tracing and tracking filamentous structures across scales: A systematic review.Computational and structural biotechnology journal · 2023Review
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Filamentous biopolymer networks in cells and tissues are routinely imaged by confocal microscopy. Image analysis methods enable quantitative study of the properties of these curvilinear networks. However, software tools to quantify the geometry and topology of these often dense 3D networks and to localize network junctions are scarce. To fill this gap, we developed a new software tool called "SOAX", which can accurately extract the centerlines of 3D biopolymer networks and identify network junctions using Stretching Open Active Contours (SOACs). It provides an open-source, user-friendly platform for network centerline extraction, 2D/3D visualization, manual editing and quantitative analysis. We propose a method to quantify the performance of SOAX, which helps determine the optimal extraction parameter values. We quantify several different types of biopolymer networks to demonstrate SOAX's potential to help answer key questions in cell biology and biophysics from a quantitative viewpoint.
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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.