Package: flowcatchR
Type: Package
Title: Tools to analyze in vivo microscopy imaging data focused on
        tracking flowing blood cells
Version: 1.47.0
Date: 2024-12-20
Authors@R: c(person("Federico", "Marini", role = c("aut", "cre"), 
        email ="marinif@uni-mainz.de", 
        comment = c(ORCID = '0000-0003-3252-7758')))
Description: 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.
License: BSD_3_clause + file LICENSE
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown
Depends: R (>= 2.10), methods, EBImage
Imports: colorRamps, abind, BiocParallel, graphics, stats, utils,
        plotly, shiny
SystemRequirements: ImageMagick
LazyData: true
URL: https://github.com/federicomarini/flowcatchR,
        https://federicomarini.github.io/flowcatchR/
BugReports: https://github.com/federicomarini/flowcatchR/issues
biocViews: Software, Visualization, CellBiology, Classification,
        Infrastructure, GUI, ShinyApps
RoxygenNote: 7.3.2
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: cmake libfftw3-dev make libmagick++-dev gsfonts
        libicu-dev libjpeg-dev libpng-dev libtiff-dev libuv1-dev
        libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:39:57 UTC
RemoteUrl: https://github.com/bioc/flowcatchR
RemoteRef: HEAD
RemoteSha: eed392f2e09fa4282106ccd1ea6337c2ea27b8c0
NeedsCompilation: no
Packaged: 2026-07-03 20:00:15 UTC; root
Author: Federico Marini [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3252-7758>)
Maintainer: Federico Marini <marinif@uni-mainz.de>