README.md

In NHPatterson/Reg3DIMS: Automated registration of sequential 2D IMS for 3D reconstruction in Cardinal

Reg3DIMS

Register sequential 2D IMS data loaded into Cardinal using NiftyReg.

Reg3DIMS extends Cardinal's excellent data structures for 3D IMS experiments registered using RNiftyReg.

Installation

#install devtools package is not already installed...
install.packages('devtools')

#install Reg3DIMS from github using devtools
library(devtools)
devtools::install_github('nhpatterson/Reg3DIMS')


#also install dependencies
install.packages('RNiftyReg')

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("EBImage")
BiocManager::install("Cardinal")

Markdown example

3D pipeline on example Mouse Brain dataset

NHPatterson/Reg3DIMS documentation built on Oct. 30, 2019, 10:04 p.m.