To begin, we want to load (or download) the packages we will need for this exercise using library:
library(tidyverse) # BiocManager::install("EBImage") library(EBImage) # install.packages("spatstat") library("spatstat") Extending the analysis in section 11.17 for all cell types This exercise asks us to analyze an image of a lymph node and evaluate the spatial dependence for all of the cell types in the lymph node. In this case, the null hypothesis is that each of the cell types are evenly distributed (via a homogenous Poisson process) throughout the lymph node.
Chapter 11 is focused on learning how to read, write, and manipulate images in R. The first sections are helping the reader understand when to apply different filters and transformations to an image and why it is necessary. It then touches on segmentation and feature extraction, two components that are utilized to simplify an image for machine learning and recognition. Finally, statistal methods are introduced to analyze spacial distributions and spatial point process is introduced on a basic level.