link.particles {flowcatchR} | R Documentation

## Links a `ParticleSet` object

### Description

Performs linking of the particles by tracking them through the frames

### Usage

    link.particles(
      particleset,
      L,
      R = 2,
      epsilon1 = 0.1,
      epsilon2 = 2,
      lambda1 = 1,
      lambda2 = 1,
      penaltyFunction = penaltyFunctionGenerator(),
      verboseOutput = FALSE,
      prog = FALSE,
      include.intensity = TRUE,
      include.area = FALSE
    )

### Arguments

`particleset` | A `ParticleSet` object
`L` | Maximum number of pixels an object can move in two consecutive frames
`R` | Linkrange, i.e. the number of consecutive frames to search for potential candidate links
`epsilon1` | A numeric value, to be used in the formula. Jitter for allowing angular displacements
`epsilon2` | A numeric value, to be used in the formula. Jitter for allowing spatial displacements
`lambda1` | A numeric value. Multiplicative factor for the penalty function
`lambda2` | A numeric value. Multiplicative factor applied to the angular displacement
`penaltyFunction` | A function structured in such a way to be applied as penalty function in the linking
`verboseOutput` | Logical, whether the output should report additional intermediate steps. For debugging use mainly
`prog` | Logical, whether the a progress bar should be shown during the tracking phase
`include.intensity` | Logical, whether to include also intensity change of the particles in the cost function calculation
`include.area` | Logical, whether to include also area change of the particles in the cost function calculation

### Value

A `LinkedParticleSet` object

### Author(s)

Federico Marini, marinif@uni-mainz.de, 2014

### References

I F Sbalzarini and P Koumoutsakos."Feature point tracking and trajectory analysis for video imaging in cell biology." In: Journal of structural biology 151.2 (Aug. 2005), pp. 182-95. ISSN: 1047-8477. DOI: 10.1016/j.jsb.2005.06.002. URL: http://www.ncbi.nlm.nih.gov/pubmed/16043363

### Examples

    data("candidate.platelets")
    tracked.platelets <- link.particles(candidate.platelets, L= 40)

[Package flowcatchR version 1.22.0 Index]