ArticleBioinformatics (Oxford, England)2020
Topological data analysis quantifies biological nano-structure from single molecule localization microscopy.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
- Adversarial Erasing Enhanced Multiple Instance Learning (siMILe): Discriminative Identification of Oligomeric Protein Structures in Single Molecule Localization Microscopy.Advanced intelligent systems (Weinheim an der Bergstrasse, Germany) · 2026Article
- Molecular mapping in DNA-PAINT via modified Gaussian Mixture Modeling.Nature communications · 2026Article
- MINFLUX nanoscopy to study the NK cell immune synapse.Methods in cell biology · 2026Article
- Enhanced spatial clustering of single-molecule localizations with graph neural networks.Nature communications · 2025Article
- HDCluster: High-Degree Graph Clustering for Robust Analysis of Single Molecule Localization Microscopy.bioRxiv : the preprint server for biology · 2025Article
- CD16a pairs form the basal molecular subunit for the NK-cell ADCC lytic synapse.Journal of immunology (Baltimore, Md. : 1950) · 2025Article
- Nanocluster-mediated signaling crosstalk between FcγR and TLR4 in macrophage inflammatory responses.Scientific reports · 2025Article
- Article
- The topology and geometry of neural representations.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Distinct mobility patterns of BRCA2 molecules at DNA damage sites.Nucleic acids research · 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
- PrestoCell: A persistence-based clustering approach for rapid and robust segmentation of cellular morphology in three-dimensional data.PloS one · 2024Article
- 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
- A framework for evaluating the performance of SMLM cluster analysis algorithms.Nature methods · 2023Article
- Advanced image-free analysis of the nano-organization of chromatin and other biomolecules by Single Molecule Localization Microscopy (SMLM).Computational and structural biotechnology journal · 2023Article
- Maximum-likelihood model fitting for quantitative analysis of SMLM data.Nature methods · 2023Article
- Recent development of computational cluster analysis methods for single-molecule localization microscopy images.Computational and structural biotechnology journal · 2023Review
- Quantitative Analysis of PcG-Associated Condensates by Stochastic Optical Reconstruction Microscopy (STORM).Methods in molecular biology (Clifton, N.J.) · 2023Article
- Cluster analysis for localisation-based data sets: dos and don'ts when quantifying protein aggregates.Frontiers in bioinformatics · 2023Review
- Introducing Diinamic, a flexible and robust method for clustering analysis in single-molecule localization microscopy.Biological imaging · 2023Article
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8 authors.
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Abstract
motivationLocalization microscopy data is represented by a set of spatial coordinates, each corresponding to a single detection, that form a point cloud. This can be analyzed either by rendering an image from these coordinates, or by analyzing the point cloud directly. Analysis of this type has focused on clustering detections into distinct groups which produces measurements such as cluster area, but has limited capacity to quantify complex molecular organization and nano-structure.
resultsWe present a segmentation protocol which, through the application of persistence-based clustering, is capable of probing densely packed structures which vary in scale. An increase in segmentation performance over state-of-the-art methods is demonstrated. Moreover we employ persistent homology to move beyond clustering, and quantify the topological structure within data. This provides new information about the preserved shapes formed by molecular architecture. Our methods are flexible and we demonstrate this by applying them to receptor clustering in platelets, nuclear pore components, endocytic proteins and microtubule networks. Both 2D and 3D implementations are provided within RSMLM, an R package for pointillist-based analysis and batch processing of localization microscopy data. AVAILABILITY AND IMPLEMENTATION: RSMLM has been released under the GNU General Public License v3.0 and is available at https://github.com/JeremyPike/RSMLM. Tutorials for this library implemented as Binder ready Jupyter notebooks are available at https://github.com/JeremyPike/RSMLM-tutorials. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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