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.
EBImage 4.40.1
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")
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")