loadImages {cytomapper} | R Documentation

## Read images into CytoImageList object

### 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 (nils.eling@dqbm.uzh.ch),

Nicolas Damond (nicolas.damond@dqbm.uzh.ch)

### 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)

[Package cytomapper version 1.2.1 Index]