ArticleNature communications2023
Super-resolved trajectory-derived nanoclustering analysis using spatiotemporal indexing.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- The Arabidopsis SPFH protein HIR2 modulates receptor signaling and plasma membrane organization.The EMBO journal · 2026Article
- A versatile nanobody platform for live and super-resolution imaging of synaptic vesicle dynamics and plasticity in rodent and human neurons.Journal of nanobiotechnology · 2026Article
- Spatiotemporal Analysis of Super-resolved Live Cell Molecular Trajectory Data Using Nanoscale Spatiotemporal Indexing Clustering.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Single Particle Tracking Photo-Activated Localization Microscopy.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Revealing plasma membrane protein dynamics in living plant cells with single-molecule tracking.Journal of experimental botany · 2025Article
- Nanoscale spatiotemporal cluster analysis of expressed and endogenous proteins.Nature protocols · 2025Review
- Fluorescent Peptide Tracers for Simultaneous Oxytocin Receptor Activation and Visualization.Angewandte Chemie (International ed. in English) · 2025Article
- NKX2-5 congenital heart disease mutations show diverse loss and gain of epigenomic, biochemical and chromatin search functions underpinning pathogenicity.bioRxiv : the preprint server for biology · 2025Article
- BDNF-dependent nano-organization of Neogenin and the WAVE regulatory complex promotes actin remodeling in dendritic spines.iScience · 2024Article
- Guidelines for naming and studying plasma membrane domains in plants.Nature plants · 2024Review
- Membrane topography and the overestimation of protein clustering in single molecule localisation microscopy - identification and correction.Communications biology · 2024Article
- Synapse-Specific Trapping of SNARE Machinery Proteins in the AnesthetizedThe Journal of neuroscience : the official journal of the Society for Neuroscience · 2024Article
- Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters.Nature communications · 2024Article
- Synapsin 2a tetramerisation selectively controls the presynaptic nanoscale organisation of reserve synaptic vesicles.Nature communications · 2024Article
- SEMORE: SEgmentation and MORphological fingErprinting by machine learning automates super-resolution data analysis.Nature communications · 2024Article
- Location, location, location: Protein kinase nanoclustering for optimised signalling output.eLife · 2024Review
- OneFlowTraX: a user-friendly software for super-resolution analysis of single-molecule dynamics and nanoscale organization.Frontiers in plant science · 2024Article
- Fear extinction is regulated by the activity of long noncoding RNAs at the synapse.Nature communications · 2023Article
- Tau forms synaptic nano-biomolecular condensates controlling the dynamic clustering of recycling synaptic vesicles.Nature communications · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
12 authors.
Funding
Abstract
Single-molecule localization microscopy techniques are emerging as vital tools to unravel the nanoscale world of living cells by understanding the spatiotemporal organization of protein clusters at the nanometer scale. Current analyses define spatial nanoclusters based on detections but neglect important temporal information such as cluster lifetime and recurrence in "hotspots" on the plasma membrane. Spatial indexing is widely used in video games to detect interactions between moving geometric objects. Here, we use the R-tree spatial indexing algorithm to determine the overlap of the bounding boxes of individual molecular trajectories to establish membership in nanoclusters. Extending the spatial indexing into the time dimension allows the resolution of spatial nanoclusters into multiple spatiotemporal clusters. Using spatiotemporal indexing, we found that syntaxin1a and Munc18-1 molecules transiently cluster in hotspots, offering insights into the dynamics of neuroexocytosis. Nanoscale spatiotemporal indexing clustering (NASTIC) has been implemented as a free and open-source Python graphic user interface.
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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.