Single Molecule Tracking Data Analysis
28 Jan 2010





​Image registration determination


For more information please contact: Dr. Dan Rolfe, Dr. Michael Hirsch.

At Octopus imaging facility advanced software pipelines and support for our range of single molecule microscopy techniques is used.

Automated registration transform determination

Exploitation of single molecule data requires the detection and measurement of fluorescent spots in each image and the tracking of these spots through time. For multidimensional (multichannel) single molecule microscopy we must also determine the transformations required to align the channels. The Octopus facility has developed an advanced, automated pipeline (link opens in a new window) to perform this analysis for the wide variety of configurations of its single molecule instrumentation suite.

This pipeline incorporates:                                                                                                                                                                                                                                                       

Interactive data analysis
  • Methods from computer vision for automated registration transform determination from bead imagesBayesian feature detection
  • Bayesian segmentation algorithms from astronomy, capable of detecting faint features in noisy data
  • Integrated handling of the wide variety of instrument channel configurations
  • An advanced visualisation application facilitates browsing, filtering, sorting and further analysis of the single molecule position and intensity traces, and their export and selection for export and further analysis

We have also developed a variety of additional analysis tools and pipelines to help with the post-analysis of single molecule tracks according to the type of experiment being performed, for example:


  • Analysis of molecular dynamics through mean-square displacement curve and diffusion analysis
  • Molecular interactions through from multi-colour tracking data
  • FLImP  – determination of molecular separations with ~5nm precision
  • FRET and polarisation – for short-range interaction detection and orientational information

​We provide expert support with the single molecule analysis aspects of your Octopus access to help you exploit our capabilities to best answer your scientific questions.

We provide access to compute resources to run these analysis.

We are currently developing infrastructure to enable more convenient, integrated access to data management and analysis tools across Octopus.


Contact: Rolfe, Daniel (STFC,RAL,CLF)