Function reference • flowcatchR

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

Reference

The flowcatchR package

Working with Frames

Working with ParticlesSet and LinkedParticleSet

Working with TrajectorySet

Working with KinematicsFeatures and KinematicsFeaturesSet