This is the released version of flowcatchR; for the devel version, see flowcatchR.
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cellsBioconductor version: Release (3.21)
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] ORCID: 0000-0003-3252-7758
Maintainer: Federico Marini <marinif at uni-mainz.de>
Citation (from within R, entercitation("flowcatchR")): Installation
To install this package, start R (version "4.5") 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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("flowcatchR")Follow Installation instructions to use this package in your R session.
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