• Learn how to read and write images in and out of R

• Learn how images are represented in R and how to manipulate them

• Understand how to apply filters and transformations to images

• Apply these skills to microscopy images of cells to do segmentation and feature extraction

• Explore spatial distributions of the position of cells

Image processing and analysis toolbox for R

• Reading and writing of image files
• Interactive image viewer
• Image manipulation, transformation and filtering
• Object detection and feature extraction

Since Bioconductor 1.8 (2006)

Original developers: Oleg Sklyar Wolfgang Huber Mike Smith Gregoire Pau

Contributors: Joseph Barry Bernd Fischer Ilia Kats Philip A. Marais

library(EBImage)

f = system.file("images", "sample.png", package="EBImage")
img = readImage(f)

display(img)

Reading images

Images can be read from local files or URLs.

bioc = readImage("http://www.bioconductor.org/images/logo/jpg/bioconductor_logo_rgb.jpg")
display(bioc)

EBImage supports JPEG, PNG and TIFF file formats. For reading proprietary microscopy image data and metadata use RBioFormats.

Displaying images

• interactive JavaScript viewer
• R's build-in plotting device

The default display method can be set by options(EBImage.display).

options(EBImage.display = "raster")

display(img, method = "raster")
text(x = 20, y = 20, label = "Parrots", adj = c(0,1), col = "orange", cex = 2)

filename = "parrots.jpg"
dev.print(jpeg, filename = filename , width = dim(img)[1], height = dim(img)[2])

file.size(filename)

## [1] 37820

Supported file formats: JPEG, PNG and TIFF.

writeImage(img, "sample.jpeg", quality = 85)

writeImage(img, "sample.tiff")
writeImage(img, "sample_compressed.tiff", compression = "deflate")

files = list.files(pattern = "sample*")
data.frame(row.names=files, size=file.size(files))

##                          size
## sample.jpeg             49688
## sample.tiff            393384
## sample_compressed.tiff 293788

str(img)

## Formal class 'Image' [package "EBImage"] with 2 slots
##   ..@ .Data    : num [1:768, 1:512] 0.447 0.451 0.463 0.455 0.463 ...
##   ..@ colormode: int 0

getClassDef("Image")

## Class "Image" [package "EBImage"]
## 
## Slots:
##                           
## Name:      .Data colormode
## Class:     array   integer
## 
## Extends: 
## Class "array", from data part
## Class "structure", by class "array", distance 2
## Class "vector", by class "array", distance 3, with explicit coerce

dim(img)

## [1] 768 512

img

## Image 
##   colorMode    : Grayscale 
##   storage.mode : double 
##   dim          : 768 512 
##   frames.total : 1 
##   frames.render: 1 
## 
## imageData(object)[1:5,1:6]
##           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
## [1,] 0.4470588 0.4627451 0.4784314 0.4980392 0.5137255 0.5294118
## [2,] 0.4509804 0.4627451 0.4784314 0.4823529 0.5058824 0.5215686
## [3,] 0.4627451 0.4666667 0.4823529 0.4980392 0.5137255 0.5137255
## [4,] 0.4549020 0.4666667 0.4862745 0.4980392 0.5176471 0.5411765
## [5,] 0.4627451 0.4627451 0.4823529 0.4980392 0.5137255 0.5411765

imageData(img)[1:3, 1:6]

##           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
## [1,] 0.4470588 0.4627451 0.4784314 0.4980392 0.5137255 0.5294118
## [2,] 0.4509804 0.4627451 0.4784314 0.4823529 0.5058824 0.5215686
## [3,] 0.4627451 0.4666667 0.4823529 0.4980392 0.5137255 0.5137255

hist(img)

range(img)

## [1] 0 1

f = system.file("images", "sample-color.png", package="EBImage")
imgcol = readImage(f)
display(imgcol)

print(imgcol, short = TRUE)

## Image 
##   colorMode    : Color 
##   storage.mode : double 
##   dim          : 768 512 3 
##   frames.total : 3 
##   frames.render: 1

nuc = readImage(system.file("images", "nuclei.tif", package="EBImage"))
print(nuc, short = TRUE)

## Image 
##   colorMode    : Grayscale 
##   storage.mode : double 
##   dim          : 510 510 4 
##   frames.total : 4 
##   frames.render: 4

display(nuc)

## The image contains more than one frame: only the first one is displayed.
## To display all frames use 'all = TRUE'.