Quantitative evaluation of methods to analyze motion changes in single-particle experiments

Gorka Muñoz-Gil (), Harshith Bachimanchi, Jesús Pineda, Benjamin Midtvedt, Gabriel Fernández-Fernández, Borja Requena, Yusef Ahsini, Solomon Asghar, Jaeyong Bae, Francisco J. Barrantes, Steen W. B. Bender, Clément Cabriel, J. Alberto Conejero, Marc Escoto, Xiaochen Feng, Rasched Haidari, Nikos S. Hatzakis, Zihan Huang, Ignacio Izeddin, Hawoong Jeong, Yuan Jiang, Jacob Kæstel-Hansen, Judith Miné-Hattab, Ran Ni, Junwoo Park, Xiang Qu, Lucas A. Saavedra, Hao Sha, Nataliya Sokolovska, Yongbing Zhang, Giorgio Volpe, Maciej Lewenstein, Ralf Metzler, Diego Krapf, Giovanni Volpe () and Carlo Manzo ()
Additional contact information
Gorka Muñoz-Gil: University of Innsbruck
Harshith Bachimanchi: University of Gothenburg
Jesús Pineda: University of Gothenburg
Benjamin Midtvedt: University of Gothenburg
Gabriel Fernández-Fernández: The Barcelona Institute of Science and Technology
Borja Requena: The Barcelona Institute of Science and Technology
Yusef Ahsini: Universitat Politècnica de València
Solomon Asghar: University College London
Jaeyong Bae: Korea Advanced Institute of Science and Technology
Francisco J. Barrantes: BIOMED UCA-CONICET
Steen W. B. Bender: University of Copenhagen
Clément Cabriel: Université PSL, CNRS
J. Alberto Conejero: Universitat Politècnica de València
Marc Escoto: Universitat Politècnica de València
Xiaochen Feng: Harbin Institute of Technology (Shenzhen)
Rasched Haidari: University of Oxford
Nikos S. Hatzakis: University of Copenhagen
Zihan Huang: Hunan University
Ignacio Izeddin: Université PSL, CNRS
Hawoong Jeong: Korea Advanced Institute of Science and Technology
Yuan Jiang: Harbin Institute of Technology (Shenzhen)
Jacob Kæstel-Hansen: University of Copenhagen
Judith Miné-Hattab: Sorbonne Université, CNRS
Ran Ni: Nanyang Technological University
Junwoo Park: Sorbonne Université, CNRS
Xiang Qu: Hunan University
Lucas A. Saavedra: BIOMED UCA-CONICET
Hao Sha: Harbin Institute of Technology (Shenzhen)
Nataliya Sokolovska: Sorbonne Université, CNRS
Yongbing Zhang: Harbin Institute of Technology (Shenzhen)
Giorgio Volpe: University College London
Maciej Lewenstein: The Barcelona Institute of Science and Technology
Ralf Metzler: University of Potsdam
Diego Krapf: Colorado State University
Giovanni Volpe: University of Gothenburg
Carlo Manzo: Universitat de Vic—Universitat Central de Catalunya (UVic-UCC)

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract The analysis of live-cell single-molecule imaging experiments can reveal valuable information about the heterogeneity of transport processes and interactions between cell components. These characteristics are seen as motion changes in the particle trajectories. Despite the existence of multiple approaches to carry out this type of analysis, no objective assessment of these methods has been performed so far. Here, we report the results of a competition to characterize and rank the performance of these methods when analyzing the dynamic behavior of single molecules. To run this competition, we implemented a software library that simulates realistic data corresponding to widespread diffusion and interaction models, both in the form of trajectories and videos obtained in typical experimental conditions. The competition constitutes the first assessment of these methods, providing insights into the current limitations of the field, fostering the development of new approaches, and guiding researchers to identify optimal tools for analyzing their experiments.

Date: 2025
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DOI: 10.1038/s41467-025-61949-x

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