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