Marker-Less Stage Drift Correction in Super-Resolution Microscopy Using the Single-Cluster PHD Filter

Isabel Schlangen, Jose Franco, Jeremie Houssineau, Eric Pitkeathly, Daniel Clark, Ihor Smal, Colin Rickman

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)
706 Downloads (Pure)


Fluorescence microscopy is a technique which allows the imaging of cellular and intracellular dynamics through the activation of fluorescent molecules attached to them. It is a very important technique because it can be used to analyze the behavior of intracellular processes in vivo in contrast to methods like electron microscopy. There are several challenges related to the extraction of meaningful information from images acquired from optical microscopes due to the low contrast between objects and background and the fact that point-like objects are observed as blurred spots due to the diffraction limit of the optical system. Another consideration is that for the study of intracellular dynamics, multiple particles must be tracked at the same time, which is a challenging task due to problems such as the presence of false positives and missed detections in the acquired data. Additionally, the objective of the microscope is not completely static with respect to the cover slip due to mechanical vibrations or thermal expansions which introduces bias in the measurements. In this paper, a Bayesian approach is used to simultaneously track the locations of objects with different motion behaviors and the stage drift using image data obtained from fluorescence microscopy experiments. Namely, detections are extracted from the acquired frames using image processing techniques, and then these detections are used to accurately estimate the particle positions and simultaneously correct the drift introduced by the motion of the sample stage. A single cluster Probability Hypothesis Density (PHD) filter with object classification is used for the estimation of the multiple target state assuming different motion behaviors. The detection and tracking methods are tested and their performance is evaluated on both simulated and real data.

Original languageEnglish
Pages (from-to)193-202
Number of pages10
JournalIEEE Journal of Selected Topics in Signal Processing
Issue number1
Early online date7 Dec 2015
Publication statusPublished - Feb 2016


  • Biomedical imaging
  • molecular imaging
  • microscopy
  • particle tracking
  • probability density function
  • estimation
  • simultaneous localization and mapping
  • filtering


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