loadImages: Read images into CytoImageList object

In cytomapper: Visualization of highly multiplexed imaging data in R

Description

Function to read in single- or multi-channel images from a specified path or file. The function returns a CytoImageList object containing one image per slot. Supported file extensions are: '.tiff', '.tif', '.png', '.jpeg', '.jpg'.

Usage

loadImages(x, pattern = NULL, ...)

Arguments

x	The function takes a variety of possible character inputs: A single file Full path and file name of an individual image file. A path A path to where image files are located. A vector of files A character vector where each entry represents an individual file.
pattern	Character inputs of the following form: A single character A pattern to search for in the specified path (regular expressions are supported). A character vector Unique entries are matched against file names in the specified path.
...	arguments passed to the readImage function.

Value

A CytoImageList object

Loading specific images

This function loads images via the readImage function and stores them in a CytoImageList object. In the simplest case, x is an image file name. If x is a path, the pattern argument can be used to select image names with certain patterns. For convenience, pattern also takes a vector of characters (e.g. a colData entry in a SingleCellExperiment object) to select by unique image names. Furthermore, a vector of image names can be provided to read in multiple images.

Author(s)

Nils Eling ([e-mail]),

Nicolas Damond ([e-mail])

See Also

readImage, for reading in individual images.

Examples

# Providing a single file
single.image <- system.file("extdata/E34_mask.tiff", package = "cytomapper")
single.image <- loadImages(single.image)

# Providing a path and pattern
path.to.images <- system.file("extdata", package = "cytomapper")
image.list <- loadImages(path.to.images, pattern = "mask.tiff")

# Providing multiple patterns
data(pancreasSCE)
path.to.images <- system.file("extdata", package = "cytomapper")
image.list <- loadImages(path.to.images, pattern = pancreasSCE$MaskName)

# Providing multiple files
list.images <- list.files(system.file("extdata", package = "cytomapper"),
                            pattern = "_mask.tiff", full.names = TRUE)
image.list <- loadImages(list.images)

cytomapper documentation built on Jan. 30, 2021, 2:01 a.m.