Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells

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Documentation for package ‘flowcatchR’ version 1.36.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

add.contours	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
addParticles	Combines the information from a raw 'Frames' object and the corresponding preprocessed one
axesInfo	Info on the dimensions of the FOV
candidate.platelets	A sample 'ParticleSet' object
channel.Frames	Channel extraction for 'objects'
computeMSD	Calculates the Mean Squared Displacement for a trajectory
crop.Frames	Cut borders of a 'Frames' object
export.Frames	Exports a 'Frames' object
export.particles	Exports a 'ParticleSet' object
extractKinematics.traj	Calculate a set of kinematics parameters from a single trajectory
flowcatchR-pkg	flowcatchR: analyzing time-lapse microscopy imaging, from detection to tracking
Frames	Constructor for a 'Frames' object
Frames-class	Frames class
initialize.LinkedParticleSet	Initialize a 'ParticleSet' object for subsequent linking/tracking
inspect.Frames	Explore the frames of a 'Frames'
kinematics	Calculate a set of kinematics parameter from a 'TrajectorySet' object, or a single parameter, or from a single trajectory (all possible combinations)
KinematicsFeatures-class	KinematicsFeatures class
KinematicsFeaturesSet-class	KinematicsFeaturesSet class
length.Frames	Compute the length of render frames in a 'Frames' object
link.particles	Links a 'ParticleSet' object
LinkedParticleSet-class	LinkedParticleSet class
matchTrajToParticles	Match trajectories to related particles.
MesenteriumSubset	A sample 'Frames' object
normalizeFrames	Normalize the values of a 'Frames' object
particles	Extracts particles from the images of a 'Frames' object.
ParticleSet-class	ParticleSet class
penaltyFunctionGenerator	Generate a penalty function
plot.TrajectorySet	3D representation of a 'TrajectorySet' object
plot2D.TrajectorySet	2D projection of a 'TrajectorySet' object
preprocess.Frames	Preprocessing function for 'Frames' objects
read.Frames	Constructor for a 'Frames' object
read.particles	Constructor for a 'ParticleSet' object
repmat	Function equivalent for MATLAB's repmat - Replicate and tile arrays
rotate.Frames	Rotates all images in a 'Frames' object
select.Frames	Extracts subsets of frames from a 'Frames' object
select.particles	Performs filtering on a 'ParticleSet' object
shinyFlow	Shiny application for exploring the features and parameters provided by 'flowcatchR'
show-method	Display conveniently a 'Frames' object
show-method	Displaying conveniently a 'KinematicsFeatures' object
show-method	Display conveniently a 'KinematicsFeatureSet' object
show-method	Display conveniently a 'LinkedParticleSet' object
show-method	Display conveniently a 'ParticleSet' object
show-method	Display conveniently a 'TrajectorySet' object
snap	Snap the features of the closest particle identified
toCartesianCoords	Converts polar coordinates to cartesian coordinates
toPolarCoords	Converts cartesian coordinates to polar coordinates
trajectories	Generate trajectories
TrajectorySet-class	TrajectorySet class