Package: flowcatchR 1.39.0

Federico Marini

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.

Authors:Federico Marini [aut, cre]

flowcatchR_1.39.0.tar.gz
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flowcatchR.pdf |flowcatchR.html✨
flowcatchR/json (API)
NEWS

# Install 'flowcatchR' in R:

install.packages('flowcatchR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/federicomarini/flowcatchr/issues

Datasets:

MesenteriumSubset - A sample 'Frames' object
candidate.platelets - A sample 'ParticleSet' object

On BioConductor:flowcatchR-1.39.0(bioc 3.20)flowcatchR-1.38.0(bioc 3.19)

bioconductor-package

24 exports 1.24 score 95 dependencies 1 mentions

Last updated 2 months agofrom:3ff81a5eb7

Exports:add.contours channel.Frames crop.Frames export.Frames export.particles Frames inspect.Frames kinematics link.particles matchTrajToParticles normalizeFrames particles penaltyFunctionGenerator plot2D.TrajectorySet preprocess.Frames read.Frames read.particles rotate.Frames select.Frames select.particles shinyFlow show snap trajectories

Dependencies:abind askpass base64enc BH BiocGenerics BiocParallel bitops bslib cachem cli codetools colorRamps colorspace commonmark cpp11 crayon crosstalk curl data.table digest dplyr EBImage evaluate fansi farver fastmap fftwtools fontawesome formatR fs futile.logger futile.options generics ggplot2 glue gtable highr htmltools htmlwidgets httpuv httr isoband jpeg jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle locfit magrittr MASS Matrix memoise mgcv mime munsell nlme openssl pillar pkgconfig plotly png promises purrr R6 rappdirs RColorBrewer Rcpp RCurl rlang rmarkdown sass scales shiny snow sourcetools stringi stringr sys tibble tidyr tidyselect tiff tinytex utf8 vctrs viridisLite withr xfun xtable yaml

r Biocpkg("flowcatchR"): A framework for tracking and analyzing flowing blood cells in time lapse microscopy images

Federico Marini, Johanna Mazur, Harald Binder

Rendered fromflowcatchr_vignette.Rmdusingknitr::rmarkdownon Jul 01 2024.

Last update: 2018-09-03
Started: 2018-02-27

Help page	Topics
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	add.contours
Combines the information from a raw 'Frames' object and the corresponding preprocessed one	addParticles
Info on the dimensions of the FOV	axesInfo
A sample 'ParticleSet' object	candidate.platelets
Channel extraction for 'objects'	channel.Frames
Calculates the Mean Squared Displacement for a trajectory	computeMSD
Cut borders of a 'Frames' object	crop.Frames
Exports a 'Frames' object	export.Frames
Exports a 'ParticleSet' object	export.particles
Calculate a set of kinematics parameters from a single trajectory	extractKinematics.traj
flowcatchR: analyzing time-lapse microscopy imaging, from detection to tracking	flowcatchR-pkg
Constructor for a 'Frames' object	Frames
Frames class	Frames-class
Initialize a 'ParticleSet' object for subsequent linking/tracking	initialize.LinkedParticleSet
Explore the frames of a 'Frames'	inspect.Frames
Calculate a set of kinematics parameter from a 'TrajectorySet' object, or a single parameter, or from a single trajectory (all possible combinations)	kinematics
KinematicsFeatures class	KinematicsFeatures-class
KinematicsFeaturesSet class	KinematicsFeaturesSet-class
Compute the length of render frames in a 'Frames' object	length.Frames
Links a 'ParticleSet' object	link.particles
LinkedParticleSet class	LinkedParticleSet-class
Match trajectories to related particles.	matchTrajToParticles
A sample 'Frames' object	MesenteriumSubset
Normalize the values of a 'Frames' object	normalizeFrames
Extracts particles from the images of a 'Frames' object.	particles
ParticleSet class	ParticleSet-class
Generate a penalty function	penaltyFunctionGenerator
3D representation of a 'TrajectorySet' object	plot.TrajectorySet
2D projection of a 'TrajectorySet' object	plot2D.TrajectorySet
Preprocessing function for 'Frames' objects	preprocess.Frames
Constructor for a 'Frames' object	read.Frames
Constructor for a 'ParticleSet' object	read.particles
Function equivalent for MATLAB's repmat - Replicate and tile arrays	repmat
Rotates all images in a 'Frames' object	rotate.Frames
Extracts subsets of frames from a 'Frames' object	select.Frames
Performs filtering on a 'ParticleSet' object	select.particles
Shiny application for exploring the features and parameters provided by 'flowcatchR'	shinyFlow
Display conveniently a 'Frames' object	show,Frames-method
Displaying conveniently a 'KinematicsFeatures' object	show,KinematicsFeatures-method
Display conveniently a 'KinematicsFeatureSet' object	show,KinematicsFeaturesSet-method
Display conveniently a 'LinkedParticleSet' object	show,LinkedParticleSet-method
Display conveniently a 'ParticleSet' object	show,ParticleSet-method
Display conveniently a 'TrajectorySet' object	show,TrajectorySet-method
Snap the features of the closest particle identified	snap
Converts polar coordinates to cartesian coordinates	toCartesianCoords
Converts cartesian coordinates to polar coordinates	toPolarCoords
Generate trajectories	trajectories
TrajectorySet class	TrajectorySet-class

Package: flowcatchR 1.39.0

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

r Biocpkg("flowcatchR"): A framework for tracking and analyzing flowing blood cells in time lapse microscopy images

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