To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("flowcatchR")

In most cases, you don't need to download the package archive at all.

flowcatchR

DOI: 10.18129/B9.bioc.flowcatchR    

This is the development version of flowcatchR; for the stable release version, see flowcatchR.

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

Bioconductor version: Development (3.6)

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>

Citation (from within R, enter citation("flowcatchR")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("flowcatchR")

Documentation

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

browseVignettes("flowcatchR")

 

PDF 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, Software, Visualization
Version 1.11.0
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License BSD_3_clause + file LICENSE
Depends R (>= 2.10), methods, EBImage
Imports rgl, colorRamps, abind, BiocParallel
LinkingTo
Suggests BiocStyle, knitr, shiny
SystemRequirements ImageMagick
Enhances
URL https://github.com/federicomarini/flowcatchR
BugReports https://github.com/federicomarini/flowcatchR/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package flowcatchR_1.11.0.tar.gz
Windows Binary flowcatchR_1.11.0.zip
Mac OS X 10.11 (El Capitan) flowcatchR_1.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/flowcatchR
Package Short Url http://bioconductor.org/packages/flowcatchR/
Package Downloads Report Download Stats

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