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

Gorka Munoz-Gil; Harshith Bachimanchi; Jesus Pineda; Benjamin Midtvedt; Gabriel Fernandez-Fernandez; Borja Requena; Yusef Ahsini; Solomon Asghar; Jaeyong Bae; Francisco J. Barrantes; Steen W. B. Bender; Clement Cabriel; J. Alberto Conejero; Marc Escoto; Xiaochen Feng; Rasched Haidari; Nikos S. Hatzakis; Zihan Huang; Ignacio Izeddin; Hawoong Jeong; Yuan Jiang; Jacob Kaestel-Hansen; Judith Mine-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; Carlo Manzo

doi:10.1038/s41467-025-61949-x

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

Gorka Munoz-Gil, Harshith Bachimanchi, Jesus Pineda, Benjamin Midtvedt, Gabriel Fernandez-Fernandez, Borja Requena, Yusef Ahsini, Solomon Asghar, Jaeyong Bae, Francisco J. Barrantes, Steen W. B. Bender, Clement Cabriel, J. Alberto Conejero, Marc Escoto, Xiaochen Feng, Rasched Haidari, Nikos S. Hatzakis, Zihan Huang, Ignacio Izeddin, Hawoong JeongYuan Jiang, Jacob Kaestel-Hansen, Judith Mine-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, Carlo Manzo

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

13 Citationer (Scopus)

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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.

Originalsprog	Engelsk
Artikelnummer	6749
Tidsskrift	Nature Communications
Vol/bind	16
Udgave nummer	1
Antal sider	17
ISSN	2041-1723
DOI	https://doi.org/10.1038/s41467-025-61949-x
Status	Udgivet - 2025

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10.1038/s41467-025-61949-xLicens: CC BY

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Munoz-Gil, G., Bachimanchi, H., Pineda, J., Midtvedt, B., Fernandez-Fernandez, G., Requena, B., Ahsini, Y., Asghar, S., Bae, J., Barrantes, F. J., Bender, S. W. B., Cabriel, C., Conejero, J. A., Escoto, M., Feng, X., Haidari, R., Hatzakis, N. S., Huang, Z., Izeddin, I., ... Manzo, C. (2025). Quantitative evaluation of methods to analyze motion changes in single-particle experiments. Nature Communications, 16(1), Artikel 6749. https://doi.org/10.1038/s41467-025-61949-x

Munoz-Gil, G, Bachimanchi, H, Pineda, J, Midtvedt, B, Fernandez-Fernandez, G, Requena, B, Ahsini, Y, Asghar, S, Bae, J, Barrantes, FJ, Bender, SWB, Cabriel, C, Conejero, JA, Escoto, M, Feng, X, Haidari, R, Hatzakis, NS, Huang, Z, Izeddin, I, Jeong, H, Jiang, Y, Kaestel-Hansen, J, Mine-Hattab, J, Ni, R, Park, J, Qu, X, Saavedra, LA, Sha, H, Sokolovska, N, Zhang, Y, Volpe, G, Lewenstein, M, Metzler, R, Krapf, D, Volpe, G & Manzo, C 2025, 'Quantitative evaluation of methods to analyze motion changes in single-particle experiments', Nature Communications, bind 16, nr. 1, 6749. https://doi.org/10.1038/s41467-025-61949-x

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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.",

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AU - Fernandez-Fernandez, Gabriel

AU - Requena, Borja

AU - Ahsini, Yusef

AU - Asghar, Solomon

AU - Bae, Jaeyong

AU - Barrantes, Francisco J.

AU - Bender, Steen W. B.

AU - Cabriel, Clement

AU - Conejero, J. Alberto

AU - Escoto, Marc

AU - Feng, Xiaochen

AU - Haidari, Rasched

AU - Hatzakis, Nikos S.

AU - Huang, Zihan

AU - Izeddin, Ignacio

AU - Jeong, Hawoong

AU - Jiang, Yuan

AU - Kaestel-Hansen, Jacob

AU - Mine-Hattab, Judith

AU - Ni, Ran

AU - Park, Junwoo

AU - Qu, Xiang

AU - Saavedra, Lucas A.

AU - Sha, Hao

AU - Sokolovska, Nataliya

AU - Zhang, Yongbing

AU - Volpe, Giorgio

AU - Lewenstein, Maciej

AU - Metzler, Ralf

AU - Krapf, Diego

AU - Volpe, Giovanni

AU - Manzo, Carlo

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AB - 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.

KW - Anomalous diffusion

KW - Plasma-membrane

KW - Brownian diffusion

KW - Cell-membrane

KW - Tracking

KW - Receptor

KW - Dimerization

KW - Molecules

KW - Models

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DO - 10.1038/s41467-025-61949-x

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