Installing package dependencies
To use the BEMOVI package, several programs need to be installed beforehand:
Check that you have Java installed on your computer, which usually comes pre-installed. Otherwise you can either install the Java environment separately, or use an ImageJ version that comes bundled with its own Java version (see ImageJ installation). Please note that both ImageJ and the ParticleLinker rely on Java to be run.
Download and install ImageJ. ImageJ is an open-source and freely available image analysis tool.
Download the LOCI Bio-formats plug-in and place the jar file in the plug-ins folder of ImageJ. The plug-in allows to open .avi or .cxd files, the only video formats currently supported by BEMOVI
Download the ParticleLinker, which is a standalone version of the ParticleTracker 3D plug-in developed by the MOSAIC group. This ParticleLinker is provided with the BEMOVI package and should be placed in a directory on the computer, where the user has administrator rights.
the BEMOVI package itself, which can either be installed from github or via the source package:
To install BEMOVI from the source package file, adapt the path and run:
#UNIX example install.packages("/Users/Frank/Dropbox/bemovi demo data/Software/bemovi_1.0.tar.gz", repos=NULL, type="source", quiet=T) # Windows example install.packages("C:/Users/Frank/Dropbox/bemovi demo data/Software/bemovi_1.0.tar.gz", repos=NULL, type="source", quiet=T)
Alternatively, to install BEMOVI from github, the devtools package is required before running the command.
There are two versions of BEMOVI:
- the latest stable release on the master branch; to get the version that contains the functionality described in the original publication, load the version tagged v1.0.2
library(devtools) install_github("pennekampster/bemovi", ref="master") # uncomment next line to install the package with the functionality as described in the published manuscript # install_github("email@example.com", ref="master")
- a development version on the develop branch that has the newest features (e.g. parallel processing capabilities), but the documentation may be incomplete as well potentially some bugs. Use it on your own risk!
library(devtools) install_github("pennekampster/bemovi", ref="develop")