Quantitative study of single molecule location estimation techniques

Opt Express. 2009 Dec 21;17(26):23352-73. doi: 10.1364/OE.17.023352.


Estimating the location of single molecules from microscopy images is a key step in many quantitative single molecule data analysis techniques. Different algorithms have been advocated for the fitting of single molecule data, particularly the nonlinear least squares and maximum likelihood estimators. Comparisons were carried out to assess the performance of these two algorithms in different scenarios. Our results show that both estimators, on average, are able to recover the true location of the single molecule in all scenarios we examined. However, in the absence of modeling inaccuracies and low noise levels, the maximum likelihood estimator is more accurate than the nonlinear least squares estimator, as measured by the standard deviations of its estimates, and attains the best possible accuracy achievable for the sets of imaging and experimental conditions that were tested. Although neither algorithm is consistently superior to the other in the presence of modeling inaccuracies or misspecifications, the maximum likelihood algorithm emerges as a robust estimator producing results with consistent accuracy across various model mismatches and misspecifications. At high noise levels, relative to the signal from the point source, neither algorithm has a clear accuracy advantage over the other. Comparisons were also carried out for two localization accuracy measures derived previously. Software packages with user-friendly graphical interfaces developed for single molecule location estimation (EstimationTool) and limit of the localization accuracy calculations (FandPLimitTool) are also discussed.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Artificial Intelligence*
  • Biopolymers / analysis*
  • Biopolymers / metabolism*
  • Image Enhancement / methods*
  • Image Interpretation, Computer-Assisted / methods*
  • Microscopy, Fluorescence / methods*
  • Molecular Probe Techniques*
  • Pattern Recognition, Automated / methods*
  • Software*


  • Biopolymers