Introduction to EBImage
10 April 2023
Abstract
EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.
Package
EBImage 4.40.1
1 Getting started
EBImage is an R package distributed as part of the Bioconductor project. To install the package, start R and enter:
install.packages("BiocManager")
BiocManager::install("EBImage")Once EBImage is installed, it can be loaded by the following command.
library("EBImage")2 Reading, displaying and writing images
Basic EBImage functionality includes reading, writing, and displaying of images. Images are read using the function readImage, which takes as input a file name or an URL. To start off, let us load a sample picture distributed with the package.
f = system.file("images", "sample.png", package="EBImage")
img = readImage(f)EBImage currently supports three image file formats: jpeg, png and tiff. This list is complemented by the RBioFormats package providing support for a much wider range of file formats including proprietary microscopy image data and metadata.
The image which we just loaded can be visualized by the function display.
display(img, method="browser")