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Quantitative evaluation of methods to analyze motion changes in single-particle experiments [Registered Report Stage 1 Protocol]

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journal contribution
posted on 2023-12-08, 12:09 authored by Gorka Muñoz-Gil, Harshith Bachimanchi, Jesus PinedaJesus Pineda, Benjamin Midtvedt, Maciej LewensteinMaciej Lewenstein, Ralf Metzler, Diego Krapf, Giovanni VolpeGiovanni Volpe, Carlo Manzo

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 have designed a competition to characterize and rank the performance of these methods when analyzing the dynamic behavior of single molecules. To run this competition, we have implemented a software library to simulate realistic data corresponding to widespread diffusion and interaction models, both in the form of trajectories and videos obtained in typical experimental conditions. The competition will constitute the first assessment of these methods, provide insights into the current limits of the field, foster the development of new approaches, and guide researchers to identify optimal tools for analyzing their experiments. 

ITEMS:  Stage 1 Registered Report Protocol 


ERC StG ComplexSwimmers [Volpe] National Science Foundation grant 2102832 [Krapf] DFG grant ME 1535/12-1 [Metzler] ERC AdG NOQIA; Ministerio de Ciencia y Innovación, Agencia Estatal de Investigaciones (PGC2018-097027-, B-I00/10.13039/501100011033, CEX2019-000910-, S/10.13039/501100011033, Plan Nacional FIDEUA, PID2019-106901GB-I00, FPI, QUANTERA MAQS, PCI2019-111828-2, QUANTERA DYNAMITE PCI2022-, 132919, Proyectos de I+D+I “Retos Colaboración”, QUSPIN RTC2019-007196-7); MICIIN with funding, from European Union NextGenerationEU(PRTRC17.I1) and by Generalitat de Catalunya; Fundació, Cellex; Fundació Mir-Puig; Generalitat de Catalunya, (European Social Fund FEDER and CERCA program,, AGAUR Grant No. 2021 SGR 01452, QuantumCAT U16-011424, co-funded by ERDF Operational Program, of Catalonia 2014-2020); Barcelona Supercomputing, Center MareNostrum (FI-2022-1-0042); EU Horizon, 2020 FET-OPEN OPTOlogic (Grant No 899794); EU, Horizon Europe Program (Grant Agreement 101080086, — NeQST), National Science Centre, Poland (Symfonia, Grant No. 2016/20/W/ST4/00314); ICFO Internal, “QuantumGaudi” project; European Union’s Horizon 2020 research and innovation program under the, Marie-Skłodowska-Curie grant agreement No 101029393, (STREDCH) and No 847648 (“La Caixa” Junior Leaders, fellowships ID100010434: LCF/BQ/PI19/11690013,, LCF/BQ/PI20/11760031, LCF/BQ/PR20/11770012,, LCF/BQ/PR21/11840013). [Lewenstein] ERC (QuantAI, Project No. 10105529) [Munoz-Gil] MCIN/AEI/10.13039/501100011033, and “ESF Investing in your future” (RYC-2015-17896), MCIN/AEI/10.13039/501100011033/ and FEDER "ERDF A way of making Europe" (BFU2017-85693-R and PID2021-125386NB-I00), MCIN/AEI/10.13039/501100011033/ and FEDER, “ERDF A way of making Europe”. (BFU2017-85693-R and PID2021-125386NB-I00) [Manzo]


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