link.particles: Links a 'ParticleSet' object

In federicomarini/flowcatchR: Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells

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, [e-mail], 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)

federicomarini/flowcatchR documentation built on Dec. 21, 2024, 8:45 p.m.