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

Share:

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 <marinif@uni-mainz.de>
License
BSD_3_clause + file LICENSE
Version
1.8.0
URLs

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