flowcatchR

DOI: 10.18129/B9.bioc.flowcatchR  

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

Bioconductor version: Release (3.17)

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]

Maintainer: Federico Marini <marinif at uni-mainz.de>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("flowcatchR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("flowcatchR")

 

HTML	R Script	flowcatchR: tracking and analyzing cells in time lapse microscopy images
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CellBiology, Classification, GUI, Infrastructure, ShinyApps, Software, Visualization
Version	1.34.0
In Bioconductor since	BioC 3.0 (R-3.1) (9 years)
License	BSD_3_clause + file LICENSE
Depends	R (>= 2.10), methods, EBImage
Imports	colorRamps, abind, BiocParallel, graphics, stats, utils, plotly, shiny
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements	ImageMagick
Enhances
URL	https://github.com/federicomarini/flowcatchR https://federicomarini.github.io/flowcatchR/
BugReports	https://github.com/federicomarini/flowcatchR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	flowcatchR_1.34.0.tar.gz
Windows Binary	flowcatchR_1.34.0.zip
macOS Binary (x86_64)	flowcatchR_1.34.0.tgz
macOS Binary (arm64)	flowcatchR_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/flowcatchR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/flowcatchR
Bioc Package Browser	https://code.bioconductor.org/browse/flowcatchR/
Package Short Url	https://bioconductor.org/packages/flowcatchR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive