R: Read images into CytoImageList object

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,
  on_disk = FALSE,
  h5FilesPath = NULL,
  BPPARAM = SerialParam(),
  ...
)

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.
`on_disk`	Logical indicating if images in form of HDF5Array objects (as .h5 files) should be stored on disk rather than in memory.
`h5FilesPath`	path to where the .h5 files for on disk representation are stored. This path needs to be defined when `on_disk = TRUE`. When files should only temporarily be stored on disk, please set `h5FilesPath = getHDF5DumpDir()`
`BPPARAM`	parameters for parallelised reading in of images. This is only recommended for very large images. See `MulticoreParam` for information on how to use multiple cores for parallelised processing.
`...`	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)

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)

# On disk representation
path.to.images <- system.file("extdata", package = "cytomapper")
image.list <- loadImages(path.to.images, pattern = "mask.tiff",
                            on_disk = TRUE, h5FilesPath = HDF5Array::getHDF5DumpDir())
                            
# Parallel processing
path.to.images <- system.file("extdata", package = "cytomapper")
image.list <- loadImages(path.to.images, pattern = "mask.tiff",
                            BPPARAM = BiocParallel::MulticoreParam())

[Package cytomapper version 1.4.1 Index]