Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 115, Issue 36, Pages 9026-9031Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1804420115
Keywords
particle tracking; machine learning; artificial neural network; bioimaging; quantitative biology
Categories
Funding
- Isaac Newton Institute for Mathematical Sciences
- National Science Foundation [DMS-1715474, DMS-1412844, DMS-1462992, DMR-1151477]
- National Institute of Health [R41GM123897]
- David and Lucile Packard Foundation [2013-39274]
- Eshelman Institute of Innovation
- Direct For Mathematical & Physical Scien [1517274] Funding Source: National Science Foundation
- Division Of Mathematical Sciences [1462992] Funding Source: National Science Foundation
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R41GM123897] Funding Source: NIH RePORTER
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Particle tracking is a powerful biophysical tool that requires conversion of large video files into position time series, i.e., traces of the species of interest for data analysis. Current tracking methods, based on a limited set of input parameters to identify bright objects, are ill-equipped to handle the spectrum of spatiotemporal heterogeneity and poor signal-to-noise ratios typically presented by submicron species in complex biological environments. Extensive user involvement is frequently necessary to optimize and execute tracking methods, which is not only inefficient but introduces user bias. To develop a fully automated tracking method, we developed a convolutional neural network for particle localization from image data, comprising over 6,000 parameters, and used machine learning techniques to train the network on a diverse portfolio of video conditions. The neural network tracker provides unprecedented automation and accuracy, with exceptionally low false positive and false negative rates on both 2D and 3D simulated videos and 2D experimental videos of difficult-to-track species.
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