Software

Software

*** u-track (multiple-particle tracking) 

u-track is a multiple-particle tracking software (written in Matlab) that is designed to:

u-track software is profiled in this issue of Nature Methods.
  1. Track dense particle fields.
  2. Close gaps in particle trajectories resulting from detection failure.
  3. Capture particle merging and splitting events resulting from occlusion or genuine aggregation and dissociation events.

Its core is based on formulating correspondence problems as linear assignment problems and searching for a globally optimal solution. The software can be called either via a Graphical User Interface or command line.

For more information, please see Jaqaman et al., Nature Methods 5, pp. 695-702 (2008).

 

*** ColocP2C (colocalization analysis)

ColocP2C is a colocalization software (written in Matlab) that is designed to:

  1. Assess colocalization between two molecular entities from multi-channel high-resolution light microscopy images when one molecule has a punctate appearance while the other has a continuous appearance.
  2. Assess the above colocalization in the context of a third molecular entity (i.e. "conditional" colocalization).

For more information, please see Maringa-Githaka et al., Journal of Cell Science 129, pp. 4175-4189 (2016).

 

*** DC-MSS (transient motion analysis)

DC-MSS is a transient motion analysis software (written in Matlab) that is designed to:

  1. Distinguish between free diffusion, confined diffusion, immobility and diffusion with drift.
  2. Segment tracks into subparts exhibiting the different motion classes.

For more information, please see Vega et al., Biophysical Journal 114, pp. 1018-1025 (2018).