add.contours: Add object contours to a 'Frames' object Creates a 'Frames'...

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

Add object contours to a Frames object Creates a Frames object containing raw information, combined with the segmented images and the relative trajectory under analysis

Description

If a TrajectorySet is provided and mode is set to trajectories, returns a Frames with all trajectories included in the IDs vector painted accordingly. If the mode is set to particles, it will just plot the particles (all) on all frames. If no TrajectorySet is provided, it will be computed with default parameters. If no binary.frames is provided, it will be computed also with default parameters

Usage

add.contours(
  raw.frames,
  binary.frames = NULL,
  trajectoryset = NULL,
  trajIDs = NULL,
  mode = "particles",
  col = NULL,
  channel = NULL
)

Arguments

raw.frames	A Frames object with raw images
binary.frames	A Frames object with preprocessed frames
trajectoryset	A TrajectorySet object
trajIDs	Numeric vector, the ID(s) of the trajectory.
mode	A character string, can assume the values particles or trajectories. Defaults to particles
col	A vector of color strings
channel	A character string, to select which channel to process

Value

A new Frames object with contours of the objects added

Author(s)

Federico Marini, [e-mail], 2014

Examples

data("MesenteriumSubset")
## Not run: 
paintedTrajectories <- add.contours(raw.frames = MesenteriumSubset, 
                                    mode = "trajectories",channel="red")
paintedParticles <- add.contours(raw.frames = MesenteriumSubset, 
                                 mode = "particles",channel="red")
inspect.Frames(paintedTrajectories)
inspect.Frames(paintedParticles)

## End(Not run)

federicomarini/flowcatchR documentation built on June 12, 2025, 3:08 p.m.