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flowcatchR

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


Bioconductor version: Release (3.18)

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

Details

biocViews CellBiology, Classification, GUI, Infrastructure, ShinyApps, Software, Visualization
Version 1.36.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License BSD_3_clause + file LICENSE
Depends R (>= 2.10), methods, EBImage
Imports colorRamps, abind, BiocParallel, graphics, stats, utils, plotly, shiny
System Requirements ImageMagick
URL https://github.com/federicomarini/flowcatchR https://federicomarini.github.io/flowcatchR/
Bug Reports https://github.com/federicomarini/flowcatchR/issues
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Suggests BiocStyle, knitr, rmarkdown
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Package Archives

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

Source Package flowcatchR_1.36.0.tar.gz
Windows Binary flowcatchR_1.36.0.zip
macOS Binary (x86_64) flowcatchR_1.36.0.tgz
macOS Binary (arm64) flowcatchR_1.36.0.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