Expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images.
Single Particle Tracking (SPT) is a well known class of tools for studying the dynamics of biological macromolecules moving inside living cells. In this paper, we focus on the problem of localization and parameter estimation given a sequence of segmented images. In the standard paradigm, the locatio...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2021-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0243115 |
| _version_ | 1818929570252849152 |
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| author | Ye Lin Sean B Andersson |
| author_facet | Ye Lin Sean B Andersson |
| author_sort | Ye Lin |
| collection | DOAJ |
| description | Single Particle Tracking (SPT) is a well known class of tools for studying the dynamics of biological macromolecules moving inside living cells. In this paper, we focus on the problem of localization and parameter estimation given a sequence of segmented images. In the standard paradigm, the location of the emitter inside each frame of a sequence of camera images is estimated using, for example, Gaussian fitting (GF), and these locations are linked to provide an estimate of the trajectory. Trajectories are then analyzed by using Mean Square Displacement (MSD) or Maximum Likelihood Estimation (MLE) techniques to determine motion parameters such as diffusion coefficients. However, the problems of localization and parameter estimation are clearly coupled. Motivated by this, we have created an Expectation Maximization (EM) based framework for simultaneous localization and parameter estimation. We demonstrate this framework through two representative methods, namely, Sequential Monte Carlo combined with Expectation Maximization (SMC-EM) and Unscented Kalman Filter combined with Expectation Maximization (U-EM). Using diffusion in two-dimensions as a prototypical example, we conduct quantitative investigations on localization and parameter estimation performance across a wide range of signal to background ratios and diffusion coefficients and compare our methods to the standard techniques based on GF-MSD/MLE. To demonstrate the flexibility of the EM based framework, we do comparisons using two different camera models, an ideal camera with Poisson distributed shot noise but no readout noise, and a camera with both shot noise and the pixel-dependent readout noise that is common to scientific complementary metal-oxide semiconductor (sCMOS) camera. Our results indicate our EM based methods outperform the standard techniques, especially at low signal levels. While U-EM and SMC-EM have similar accuracy, U-EM is significantly more computationally efficient, though the use of the Unscented Kalman Filter limits U-EM to lower diffusion rates. |
| first_indexed | 2024-12-20T03:46:54Z |
| format | Article |
| id | doaj.art-c45235d32f6c4533b02345c7fc933157 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-20T03:46:54Z |
| publishDate | 2021-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-c45235d32f6c4533b02345c7fc9331572022-12-21T19:54:35ZengPublic Library of Science (PLoS)PLoS ONE1932-62032021-01-01165e024311510.1371/journal.pone.0243115Expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images.Ye LinSean B AnderssonSingle Particle Tracking (SPT) is a well known class of tools for studying the dynamics of biological macromolecules moving inside living cells. In this paper, we focus on the problem of localization and parameter estimation given a sequence of segmented images. In the standard paradigm, the location of the emitter inside each frame of a sequence of camera images is estimated using, for example, Gaussian fitting (GF), and these locations are linked to provide an estimate of the trajectory. Trajectories are then analyzed by using Mean Square Displacement (MSD) or Maximum Likelihood Estimation (MLE) techniques to determine motion parameters such as diffusion coefficients. However, the problems of localization and parameter estimation are clearly coupled. Motivated by this, we have created an Expectation Maximization (EM) based framework for simultaneous localization and parameter estimation. We demonstrate this framework through two representative methods, namely, Sequential Monte Carlo combined with Expectation Maximization (SMC-EM) and Unscented Kalman Filter combined with Expectation Maximization (U-EM). Using diffusion in two-dimensions as a prototypical example, we conduct quantitative investigations on localization and parameter estimation performance across a wide range of signal to background ratios and diffusion coefficients and compare our methods to the standard techniques based on GF-MSD/MLE. To demonstrate the flexibility of the EM based framework, we do comparisons using two different camera models, an ideal camera with Poisson distributed shot noise but no readout noise, and a camera with both shot noise and the pixel-dependent readout noise that is common to scientific complementary metal-oxide semiconductor (sCMOS) camera. Our results indicate our EM based methods outperform the standard techniques, especially at low signal levels. While U-EM and SMC-EM have similar accuracy, U-EM is significantly more computationally efficient, though the use of the Unscented Kalman Filter limits U-EM to lower diffusion rates.https://doi.org/10.1371/journal.pone.0243115 |
| spellingShingle | Ye Lin Sean B Andersson Expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images. PLoS ONE |
| title | Expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images. |
| title_full | Expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images. |
| title_fullStr | Expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images. |
| title_full_unstemmed | Expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images. |
| title_short | Expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images. |
| title_sort | expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images |
| url | https://doi.org/10.1371/journal.pone.0243115 |
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