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

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Documentation for package ‘flowcatchR’ version 1.21.2

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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