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; Carlo Manzo

doi:10.1038/s41467-025-61949-x

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^*, Carlo Manzo^*

^*Corresponding author for this work

University of Innsbruck
University of Gothenburg
ICFO-The Institute of Photonics Sciences
Polytechnic University of Valencia
University College London
Korea Advanced Institute of Science and Technology
Consejo Nacional de Investigaciones Científicas y Técnicas
University of Copenhagen
Université PSL
Harbin Institute of Technology
University of Oxford
Hunan University
Sorbonne Université
Nanyang Technological University
ICREA
University of Potsdam
Asia Pacific Center for Theoretical Physics
Colorado State University
The University of Vic - Central University of Catalonia
Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central

Research output: Contribution to journal › Article › peer-review

28 Scopus citations

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.

Original language	English
Article number	6749
Journal	Nature Communications
Volume	16
Issue number	1
DOIs	https://doi.org/10.1038/s41467-025-61949-x
State	Published - Dec 2025
Externally published	Yes

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Muñoz-Gil, G., Bachimanchi, H., Pineda, J., Midtvedt, B., Fernández-Fernández, 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), Article 6749. https://doi.org/10.1038/s41467-025-61949-x

@article{b009be51a9cb4151be75a05a88fd6747,

title = "Quantitative evaluation of methods to analyze motion changes in single-particle experiments",

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.",

author = "Gorka Mu{\~n}oz-Gil and Harshith Bachimanchi and Jes{\'u}s Pineda and Benjamin Midtvedt and Gabriel Fern{\'a}ndez-Fern{\'a}ndez and Borja Requena and Yusef Ahsini and Solomon Asghar and Jaeyong Bae and Barrantes, \{Francisco J.\} and Bender, \{Steen W.B.\} and Cl{\'e}ment Cabriel and Conejero, \{J. Alberto\} and Marc Escoto and Xiaochen Feng and Rasched Haidari and Hatzakis, \{Nikos S.\} and Zihan Huang and Ignacio Izeddin and Hawoong Jeong and Yuan Jiang and Jacob K{\ae}stel-Hansen and Judith Min{\'e}-Hattab and Ran Ni and Junwoo Park and Xiang Qu and Saavedra, \{Lucas A.\} and Hao Sha and Nataliya Sokolovska and Yongbing Zhang and Giorgio Volpe and Maciej Lewenstein and Ralf Metzler and Diego Krapf and Giovanni Volpe and Carlo Manzo",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

month = dec,

doi = "10.1038/s41467-025-61949-x",

language = "英语",

volume = "16",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

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Muñoz-Gil, G, Bachimanchi, H, Pineda, J, Midtvedt, B, Fernández-Fernández, 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, Kæstel-Hansen, J, Miné-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, vol. 16, no. 1, 6749. https://doi.org/10.1038/s41467-025-61949-x

TY - JOUR

T1 - Quantitative evaluation of methods to analyze motion changes in single-particle experiments

AU - Muñoz-Gil, Gorka

AU - Bachimanchi, Harshith

AU - Pineda, Jesús

AU - Midtvedt, Benjamin

AU - Fernández-Fernández, Gabriel

AU - Requena, Borja

AU - Ahsini, Yusef

AU - Asghar, Solomon

AU - Bae, Jaeyong

AU - Barrantes, Francisco J.

AU - Bender, Steen W.B.

AU - Cabriel, Clément

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 - Kæstel-Hansen, Jacob

AU - Miné-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

PY - 2025/12

Y1 - 2025/12

N2 - 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.

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.

UR - https://www.scopus.com/pages/publications/105011936701

U2 - 10.1038/s41467-025-61949-x

DO - 10.1038/s41467-025-61949-x

M3 - 文章

C2 - 40695819

AN - SCOPUS:105011936701

SN - 2041-1723

VL - 16

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 6749

ER -

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

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