Optimal diffusion coefficient estimation in single-particle tracking

Michalet, Xavier; Berglund, Andrew J.

doi:10.1103/physreve.85.061916

Cited by 253 publications

(378 citation statements)

References 39 publications

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“…For example, the anomalous vs. standard diffusion question can be hard to resolve using a single trajectory when one only has access to a time series spanning ≈ 1 − 5 s and measurement noise is significant relative to thermal fluctuations [18][19][20] (this noise is sometimes referred to as "localization noise" [22] in the SPT literature). Robustness against questionable localization noise assumptions is desirable since this noise is difficult to accurately quantify in many experiments [14,[22][23][24] despite its potential heavy influence on parameter estimation, hypothesis testing, and other model diagnostics [25][26][27]. In addition, methods not requiring ensemble averaging (i.e., those capable of carrying out tests with a single trajectory) are of interest since the effective dynamics experienced in vivo can be heterogeneous due to varying local micro-environments [14,19,20].…”

Section: Introductionmentioning

confidence: 99%

Robust hypothesis tests for detecting statistical evidence of two-dimensional and three-dimensional interactions in single-molecule measurements

2014

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A variety of experimental techniques have improved the 2D and 3D spatial resolution that can be extracted from in vivo single-molecule measurements. This enables researchers to quantitatively infer the magnitude and directionality of forces experienced by biomolecules in their native cellular environments. Situations where such forces are biologically relevant range from mitosis to directed transport of protein cargo along cytoskeletal structures. Models commonly applied to quantify single-molecule dynamics assume that effective forces and velocity in the x, y (or x, y, z) directions are statistically independent, but this assumption is physically unrealistic in many situations. We present a hypothesis testing approach capable of determining if there is evidence of statistical dependence between positional coordinates in experimentally measured trajectories; if the hypothesis of independence between spatial coordinates is rejected, then a new model accounting for 2D (3D) interactions should be considered to more faithfully represent the underlying experimental kinetics. The technique is robust in the sense that 2D (3D) interactions can be detected via statistical hypothesis testing even if there is substantial inconsistency between the physical particle's actual noise sources and the simplified model's assumed noise structure. For example, 2D (3D) interactions can be reliably detected even if the researcher assumes normal diffusion, but the experimental data experiences "anomalous diffusion" and/or is subjected to a measurement noise characterized by a distribution differing from that assumed by the fitted model. The approach is demonstrated on control simulations and on experimental data (IFT88 directed transport in the primary cilium).

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Section: Introductionmentioning

confidence: 99%

Robust hypothesis tests for detecting statistical evidence of two-dimensional and three-dimensional interactions in single-molecule measurements

2014

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“…Berglund (Michalet and Berglund, 2012 that fitting a sum of normal distributions to the LogD histogram is equivalent to fitting a sum 1069 of log-normal distributions to the D histogram. We also note here, that in a theoretical study 1070 Michalet previously showed that the distribution of diffusion constants is approximately 1071…”

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confidence: 99%

Spot-On: robust model-based analysis of single-particle tracking experiments

Hansen

Woringer

Grimm

et al. 2017

Preprint

115

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2 ABSTRACT 27Single-particle tracking (SPT) has become an important method to bridge 28 biochemistry and cell biology since it allows direct observation of protein binding and 29 diffusion dynamics in live cells. However, accurately inferring information from SPT studies 30 is challenging due to biases in both data analysis and experimental design. To address analysis 31 bias, we introduce "Spot-On", an intuitive web-interface. Spot-On implements a kinetic 32 modeling framework that accounts for known biases, including molecules moving out-of-33 focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule 34 trajectories. To minimize inherent experimental biases, we implement and validate 35 stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking 36 errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On 37 outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian 38 cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently 39 and robustly infers subpopulation fractions and diffusion constants. 40

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“…The optimal resolution is application-dependent: single-molecule localization may not need as good a temporal resolution as for studying singlemolecule conformational dynamic using FRET, for instance. In fact, the optimal choice of temporal resolution may sometimes be counterintuitive, as in the case of diffusion coefficient measurements, where longer integration times are in general always preferable [135].…”

Section: (D) Detectors Used For Wide Field Single-molecule Imagingmentioning

confidence: 99%

Development of new photon-counting detectors for single-molecule fluorescence microscopy

Michalet

Colyer

Scalia

et al. 2013

Phil. Trans. R. Soc. B

106

121

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Two optical configurations are commonly used in single-molecule fluorescence microscopy: point-like excitation and detection to study freely diffusing molecules, and wide field illumination and detection to study surface immobilized or slowly diffusing molecules. Both approaches have common features, but also differ in significant aspects. In particular, they use different detectors, which share some requirements but also have major technical differences. Currently, two types of detectors best fulfil the needs of each approach: single-photon-counting avalanche diodes (SPADs) for point-like detection, and electron-multiplying charge-coupled devices (EMCCDs) for wide field detection. However, there is room for improvements in both cases. The first configuration suffers from low throughput owing to the analysis of data from a single location. The second, on the other hand, is limited to relatively low frame rates and loses the benefit of single-photon-counting approaches. During the past few years, new developments in point-like and wide field detectors have started addressing some of these issues. Here, we describe our recent progresses towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. We also discuss our development of large area photon-counting cameras achieving subnanosecond resolution for fluorescence lifetime imaging applications at the single-molecule level

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Optimal diffusion coefficient estimation in single-particle tracking

Cited by 253 publications

References 39 publications

Robust hypothesis tests for detecting statistical evidence of two-dimensional and three-dimensional interactions in single-molecule measurements

Robust hypothesis tests for detecting statistical evidence of two-dimensional and three-dimensional interactions in single-molecule measurements

Spot-On: robust model-based analysis of single-particle tracking experiments

Development of new photon-counting detectors for single-molecule fluorescence microscopy

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