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 (3.21)
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:
Maintainer: Federico Marini <marinif at uni-mainz.de>
citation("flowcatchR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBiology, Classification, GUI, Infrastructure, ShinyApps, Software, Visualization |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (10 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | flowcatchR_1.41.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |