ArticleMethods (San Diego, Calif.)2020
Quantification of trans-synaptic protein alignment: A data analysis case for single-molecule localization microscopy.
Article in Methods (San Diego, Calif.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- 3D Expansion-PALM (PhotoActivated Localization Microscopy) Dissects Protein-Protein Interactions Down to the Molecular Scale in Bacteria.Microorganisms · 2026Article
- Trans-synaptic molecular context of NMDA receptor nanodomains.Nature communications · 2025Article
- Chronic benzodiazepine treatment triggers gephyrin scaffold destabilization and GABAFrontiers in cellular neuroscience · 2025Article
- Single-shot 20-fold expansion microscopy.Nature methods · 2024Article
- Distinct active zone protein machineries mediate CaNature neuroscience · 2024Article
- Distinct SAP102 and PSD-95 Nano-organization Defines Multiple Types of Synaptic Scaffold Protein Domains at Single Synapses.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2024Article
- RNA-binding properties orchestrate TDP-43 homeostasis through condensate formation in vivo.Nucleic acids research · 2024Article
- Structural and functional reorganization of inhibitory synapses by activity-dependent cleavage of neuroligin-2.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular definition of distinct active zone protein machineries for CabioRxiv : the preprint server for biology · 2023Article
- Distinct SAP102 and PSD-95 nano-organization defines multiple types of synaptic scaffold protein domains at single synapses.bioRxiv : the preprint server for biology · 2023Article
- Differential nanoscale organization of excitatory synapses onto excitatory vs inhibitory neurons.bioRxiv : the preprint server for biology · 2023Article
- Neurexin-3 subsynaptic densities are spatially distinct from Neurexin-1 and essential for excitatory synapse nanoscale organization in the hippocampus.Nature communications · 2023Article
- Revealing nanostructures in brain tissue via protein decrowding by iterative expansion microscopy.Nature biomedical engineering · 2022Article
- Neuroligin-3 confines AMPA receptors into nanoclusters, thereby controlling synaptic strength at the calyx of Held synapses.Science advances · 2022Article
- A coordinate-based co-localization index to quantify and visualize spatial associations in single-molecule localization microscopy.Scientific reports · 2022Article
- The Structural Basis of Long-Term Potentiation in Hippocampal Synapses, Revealed by Electron Microscopy Imaging of Lanthanum-Induced Synaptic Vesicle Recycling.Frontiers in cellular neuroscience · 2022Article
- Correlative Assembly of Subsynaptic Nanoscale Organizations During Development.Frontiers in synaptic neuroscience · 2022Article
- Subsynaptic positioning of AMPARs by LRRTM2 controls synaptic strength.Science advances · 2021Article
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3 authors.
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Abstract
Nanoscale distribution of proteins and their relative positioning within a defined subcellular region are key to their physiological functions. Thanks to the super-resolution imaging methods, especially single-molecule localization microscopy (SMLM), mapping the three-dimensional distribution of multiple proteins has been easier and more efficient than ever. Nevertheless, in spite of the many tools available for efficient localization detection and image rendering, it has been a challenge to quantitatively analyze the 3D distribution and relative positioning of proteins in these SMLM data. Here, using heterogeneously distributed synaptic proteins as examples, we describe in detail a series of analytical methods including detection of nanoscale density clusters, quantification of the trans-synaptic alignment between these protein densities, and automatic en face projection and averaging. These analyses were performed within customized Matlab routines and we make the full scripts available. The concepts behind these analytical methods and the scripts can be adapted for quantitative analysis of spatial organization of other macromolecular complexes.
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