loadImages | R Documentation |
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', ".h5".
loadImages(
x,
pattern = NULL,
single_channel = FALSE,
on_disk = FALSE,
h5FilesPath = NULL,
name = NULL,
BPPARAM = SerialParam(),
...
)
x |
The function takes a variety of possible character inputs:
|
pattern |
Character inputs of the following form:
|
single_channel |
logical indicating if each file per folder contains
a single channel. These files will be read in and stitched together to
form a single multi-channel image. For this, |
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 |
name |
(if reading in .h5 files) a single character, a character vector
of length equal to the length of x or NULL. See details for how to set
|
BPPARAM |
parameters for parallelised reading in of images.
This is only recommended for very large images.
See |
... |
arguments passed to the |
A CytoImageList object
To correctly read in the original integer values of 16-bit, the as.is =
TRUE
parameter needs to be added to the function call. This will prevent the
readTIFF
function to re-scale integer values.
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.
When reading in .h5 files by default the loadImages
function will
try to read in the dataset with the same name as the .h5 file from within
the file. If datasets are stored with different names, the name
argument must be specified. This can either be a single character if datasets
across all files are named the same or a character vector of the same length
as x
indicating the dataset name within each .h5 file. By default,
the images/datasets are not read into memory when stored in .h5 files.
Nils Eling (nils.eling@dqbm.uzh.ch),
Nicolas Damond (nicolas.damond@dqbm.uzh.ch)
readImage
, for reading in individual images.
# 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())
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