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

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.

AuthorFederico Marini [aut, cre]
Date of publicationNone
MaintainerFederico Marini <marinif@uni-mainz.de>
LicenseBSD_3_clause + file LICENSE
Version1.8.0
https://github.com/federicomarini/flowcatchR

View on Bioconductor

Man pages

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

KinematicsFeaturesSet-class: KinematicsFeaturesSet

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

Files in this package

flowcatchR/.travis.yml
flowcatchR/DESCRIPTION
flowcatchR/LICENSE
flowcatchR/NAMESPACE
flowcatchR/NEWS
flowcatchR/R
flowcatchR/R/AllClasses.R flowcatchR/R/AllGenerics.R flowcatchR/R/auxiliary.R flowcatchR/R/flowcatchR.R flowcatchR/R/kinematics.R flowcatchR/R/postprocessing.R flowcatchR/R/preprocessing.R flowcatchR/R/show-methods.R flowcatchR/R/tracking.R flowcatchR/R/trajectories.R
flowcatchR/README.md
flowcatchR/build
flowcatchR/build/vignette.rds
flowcatchR/data
flowcatchR/data/MesenteriumSubset.RData
flowcatchR/data/candidate.platelets.RData
flowcatchR/data/datalist
flowcatchR/inst
flowcatchR/inst/doc
flowcatchR/inst/doc/flowcatchR-vignette.R
flowcatchR/inst/doc/flowcatchR-vignette.Rnw
flowcatchR/inst/doc/flowcatchR-vignette.pdf
flowcatchR/inst/extdata
flowcatchR/inst/extdata/snapExp.jpg
flowcatchR/inst/extdata/template_DetectionOfTransmigrationEvents.ipynb
flowcatchR/inst/extdata/template_flowcatchR_vignetteSummary.ipynb
flowcatchR/inst/shiny
flowcatchR/inst/shiny/ABOUT.md
flowcatchR/inst/shiny/server.R
flowcatchR/inst/shiny/ui.R
flowcatchR/inst/shiny/www
flowcatchR/inst/shiny/www/logo_bioconductor.gif
flowcatchR/inst/shiny/www/logo_unimedizin.png
flowcatchR/man
flowcatchR/man/Frames-class.Rd flowcatchR/man/Frames.Rd flowcatchR/man/KinematicsFeatures-class.Rd flowcatchR/man/KinematicsFeaturesSet-class.Rd flowcatchR/man/LinkedParticleSet-class.Rd flowcatchR/man/MesenteriumSubset.Rd flowcatchR/man/ParticleSet-class.Rd flowcatchR/man/TrajectorySet-class.Rd flowcatchR/man/add.contours.Rd flowcatchR/man/addParticles.Rd flowcatchR/man/axesInfo.Rd flowcatchR/man/candidate.platelets.Rd flowcatchR/man/channel.Frames.Rd flowcatchR/man/computeMSD.Rd flowcatchR/man/crop.Frames.Rd flowcatchR/man/export.Frames.Rd flowcatchR/man/export.particles.Rd flowcatchR/man/extractKinematics.traj.Rd flowcatchR/man/flowcatchR.Rd flowcatchR/man/initialize.LinkedParticleSet.Rd flowcatchR/man/inspect.Frames.Rd flowcatchR/man/kinematics.Rd flowcatchR/man/length.Frames.Rd flowcatchR/man/link.particles.Rd flowcatchR/man/matchTrajToParticles.Rd flowcatchR/man/normalizeFrames.Rd flowcatchR/man/particles.Rd flowcatchR/man/penaltyFunctionGenerator.Rd flowcatchR/man/plot.TrajectorySet.Rd flowcatchR/man/plot2D.TrajectorySet.Rd flowcatchR/man/preprocess.Frames.Rd flowcatchR/man/read.Frames.Rd flowcatchR/man/read.particles.Rd flowcatchR/man/repmat.Rd flowcatchR/man/rotate.Frames.Rd flowcatchR/man/select.Frames.Rd flowcatchR/man/select.particles.Rd flowcatchR/man/shinyFlow.Rd flowcatchR/man/show-Frames-method.Rd flowcatchR/man/show-KinematicsFeatures-method.Rd flowcatchR/man/show-KinematicsFeaturesSet-method.Rd flowcatchR/man/show-LinkedParticleSet-method.Rd flowcatchR/man/show-ParticleSet-method.Rd flowcatchR/man/show-TrajectorySet-method.Rd flowcatchR/man/snap.Rd flowcatchR/man/toCartesianCoords.Rd flowcatchR/man/toPolarCoords.Rd flowcatchR/man/trajectories.Rd
flowcatchR/vignettes
flowcatchR/vignettes/flowcatchR-vignette.Rnw
flowcatchR/vignettes/flowcatchR.bib

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