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

## Documentation for package ‘flowcatchR’ version 1.21.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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