flowcatchR is a set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides the steps from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations (e.g. how good the segmentation was). It allows investigating the issue of tracking flowing cells such as in blood vessels, to categorize the particles in flowing, rolling and adherent. This classification is applied in the study of phenomena such as hemostasis and study of thrombosis development. Moreover, flowcatchR presents an integrated workflow solution, based on the integration with a Shiny App and Jupyter notebooks, which is delivered alongside the package, and can enable fully reproducible bioimage analysis in the R environment.
|Author||Federico Marini [aut, cre]|
|Date of publication||None|
|Maintainer||Federico Marini <firstname.lastname@example.org>|
|License||BSD_3_clause + file LICENSE|
add.contours: Add object contours to a 'Frames' object
addParticles: Combines the information from a raw 'Frames' object and the...
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...
flowcatchR: flowcatchR: analyzing time-lapse microscopy imaging, from...
Frames: Constructor for a 'Frames' object
Frames-class: Frames class
initialize.LinkedParticleSet: Initialize a 'ParticleSet' object for subsequent...
inspect.Frames: Explore the frames of a 'Frames'
kinematics: Calculate a set of kinematics parameter from a...
KinematicsFeatures-class: KinematicsFeatures class
length.Frames: Compute the length of render frames in a 'Frames' object
LinkedParticleSet-class: LinkedParticleSet class
link.particles: Links a 'ParticleSet' object
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
plot2D.TrajectorySet: 2D projection of a 'TrajectorySet' object
plot.TrajectorySet: 3D representation 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...
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...
show-Frames-method: Display conveniently a 'Frames' object
show-KinematicsFeatures-method: Displaying conveniently a 'KinematicsFeatures' object
show-KinematicsFeaturesSet-method: Display conveniently a 'KinematicsFeatureSet' object
show-LinkedParticleSet-method: Display conveniently a 'LinkedParticleSet' object
show-ParticleSet-method: Display conveniently a 'ParticleSet' object
show-TrajectorySet-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