In baumer-lab/cranium: Quantifying Radial Bridge Structures

An R package to quantify radial bridge images

Installation

cranium depends on the rhdf5 package for reading HDF5 files, but this package is not available on CRAN. You must install it from Bioconductor. To do this, you have to run the following code once:

install.packages("BiocInstaller",
                 repos = "http://bioconductor.org/packages/3.4/bioc")
source("https://bioconductor.org/biocLite.R")
biocLite("rhdf5")

Then, you can install cranium from GitHub using the following commands:

install.packages("devtools")
devtools::install_github("beanumber/cranium")

Download sample data

To download sample data, You Too and WildType, you can run:

youtoo <- download_youtoo_data("folder") #where folder is the location you want to store the You Too data
wildtype <- download_wildtype_data("folder") #where folder is the location you want to store the Wild Type data
youtoo[[1]] #first you too data sample

Once the above is ran, the files are saved in a list and in the folder you set, each data sample can be indivudually picked from list by indexing.

Plot a 3D image of a brain

Now, you can simply point to a raw HDF5 file, and quickly render a 3D image of the data, along with our model of it.

file <- "~/Data/barresi/AT_1_Probabilities.h5"
library(cranium)
library(tidyverse)
tidy_brain <- file %>%
  read_h5() %>%
  tidy()
plot3d(tidy_brain)

baumer-lab/cranium documentation built on Nov. 3, 2019, 2:07 p.m.