ImageJ User & Developer Conference 2015: http://imagej.net/Conference_2015
Bio7 – Statistical image analysis and reproducible reports with ImageJ and R
Bio7 2.3 - now available here: http://sourceforge.net/projects/bio7/
Simply unzip the archive of Bio7 2.3 (Windows, Linux) in your preferred OS location. The MacOSX version can be installed easily with the available *.dmg file installer.
To start the application simply double click on the Bio7 binary file.
You can download and update this repository if you install the Eclipse GIT plugin into Bio7:
Help->Install New Software...->Select Eclipse Mars repository->Collaboration->Select 'Eclipse GIT Team Provider' see: https://youtu.be/W15SUGBmG3M
The Windows version of Bio7 is bundled with R and Rserve. No extra installation is needed.
For Linux and MacOSX R and Rserve has to be installed! Bio7 will fetch the default paths from the OS System PATH (so hopefully no other adjustments have to be made).
Download R at: https://www.r-project.org/
Rserve has to be available in cooperative mode which can be installed from the Bio7 Bitbucket website from within R with:
MacOSX:
Open R and type:
install.packages("https://bitbucket.org/maustenfeld/bio7-new/downloads/Rserve_1.8-4_Mac_cooperative.tgz", repos=NULL)
Linux (compiled with Linux Mint 17.2):
Open R and type:
install.packages("https://bitbucket.org/maustenfeld/bio7-new/downloads/Rserve_1.8-4_Linux_cooperative.tar.gz", repos=NULL)
For this workshop you have to install some R packages which will be used during the workshop.
knitr package: http://yihui.name/knitr/
spatstat package: http://spatstat.github.io/
formatR package: https://cran.r-project.org/web/packages/formatR/index.html
rmarkdown package: http://rmarkdown.rstudio.com/ (pandoc installation required - see Special Software!)
rgdal package: https://cran.r-project.org/web/packages/rgdal/index.html
maptools package: https://cran.r-project.org/web/packages/maptools/index.html
sp package: https://cran.r-project.org/web/packages/sp/index.html
raster package: https://cran.r-project.org/web/packages/raster/index.html
ggplot2 package: http://ggplot2.org/
You can install the packages e.g. with the following script (you can find the R script in the repository, too):
packagesIJWorkshop<-c("knitr","formatR","rmarkdown","sp", "maptools", "rgdal", "spatstat","raster","ggplot2")
install.packages(packagesIJWorkshop, dep=TRUE, repos="http://cran.us.r-project.org")
Linux only: Note that the R packages for Linux will be compiled. An installation of 'gfortran' and 'g++' is necessary if not by default. For the packages 'spatstat' and 'rgdal' the following Linux libraries have to be installed, too.
GDAL: gdal,libgdal-dev,libproj-dev
spatstat: libblas-dev,liblapack
For the rmarkdown package pandoc (http://pandoc.org/) has to be installed.
Download at: https://github.com/jgm/pandoc/releases/latest
After the binary installation it is often necessary to update the search path in R to include the installation directory of pandoc.
MacOSX Add to the OS PATH. Else type in the R console:
Sys.setenv(PATH="/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:$HOME/bin")
or with the LaTeX path added:
Sys.setenv(PATH="/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:$HOME/bin")
Linux After installation available. Else type in the R console:
Sys.setenv(PATH="/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:$HOME/bin")
Windows Add pandoc path to the Windows PATH variable (evtl restart). Else type in the R console:
Sys.setenv(PATH=paste(Sys.getenv("PATH"),"C:/pandoc", sep=""))
The commands can be copied and saved for each startup (only if necessary) in the R preferences textfield:
R->Preferences->Rserve Preferences->R startup commands
To use LaTeX with Bio7 please install a LaTeX environment e.g.
Windows: MiKeTX (http://miktex.org/)
MacOSX: MacTeX (https://tug.org/mactex/)
Linux: TeX Live (http://www.tug.org/texlive/)
Then adjust the Bio7 path to the pdflatex binary (only necessary if not on the OS path!):
R->Preferences->Rserve preferences->pdflatex path
To get the installation location folder on Linux or on MacOSX type:
which pdflatex
For Windows MikeTeX pdflatex can be typically found at:
C:\Program Files (x86)\MiKTeX 2.9\miktex\bin
Bio7: http://bio7.org
spatstat website: http://spatstat.github.io/
spatstat workshop notes: https://research.csiro.au/software/r-workshop-notes/
R Markdown: http://rmarkdown.rstudio.com/
useR R markdown tutorial: https://github.com/daroczig/user2015-markdown-tutorial