Super-resolved trajectory-derived nanoclustering analysis using spatiotemporal indexing

• Published in: Nature communications Vol. 14; no. 1; pp. 3353 - 16
• Main Authors: Wallis, Tristan P., Jiang, Anmin, Young, Kyle, Hou, Huiyi, Kudo, Kye, McCann, Alex J., Durisic, Nela, Joensuu, Merja, Oelz, Dietmar, Nguyen, Hien, Gormal, Rachel S., Meunier, Frédéric A.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 08.06.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/1564; 631/114/2404; 631/1647/328/2238; Algorithms; Cell Membrane - metabolism; Cells (biology); Clustering; Computer & video games; Exocytosis; Humanities and Social Sciences; Indexing; Localization; Microscopy; Molecular trajectories; multidisciplinary; Nanoclusters; Proteins; Proteins - metabolism; Science; Science (multidisciplinary); Spatial analysis; Spatio-Temporal Analysis; Syntaxin 1; Trajectory analysis
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-38866-y

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. Existing single-molecule localization microscopy analyses overlook important temporal information in living cells. Here, the authors report nanoscale spatiotemporal indexing clustering (NASTIC), which leverages a video game algorithm to fast-track the investigation of the complex temporal dynamics of protein clustering.