LoadImages: Function used to read HE images in jpeg or png format

In jbergenstrahle/STUtility: Analysis and visualization of Spatial Transcriptomics data

Function used to read HE images in jpeg or png format

Description

Function used to read HE images in jpeg or png format

Usage

LoadImages(
  object,
  image.paths = NULL,
  xdim = 400,
  crop.to.fiducials = FALSE,
  crop.scale.factors = c(9, 10, 10, 8),
  verbose = TRUE,
  time.resolve = FALSE
)

## S3 method for class 'Staffli'
LoadImages(
  object,
  image.paths = NULL,
  xdim = 400,
  crop.to.fiducials = FALSE,
  crop.scale.factors = c(9, 10, 10, 8),
  verbose = TRUE,
  time.resolve = TRUE
)

## S3 method for class 'Seurat'
LoadImages(
  object,
  image.paths = NULL,
  xdim = 400,
  crop.to.fiducials = FALSE,
  crop.scale.factors = c(9, 10, 10, 8),
  verbose = TRUE,
  time.resolve = TRUE
)

Arguments

object	Seurat or Staffli object
image.paths	Paths to HE images. This is only required if image paths are missing in the Seurat object.
xdim	Sets the pixel width for scaling, e.g. 400 (maximum allowed width is 2000 pixels)
crop.to.fiducials	Set to TRUE if you want to crop out background from the images outside the fiducials.
crop.scale.factors	Numeric vector of length 4 providing a scaling factor for each side of the image. The scaling factors define the number of spot widths away from the capture area to include in the cropped image if 'crop.to.fiducials' is set to TRUE. The default values are c(9, 10, 10, 8) which corresponds to left, top, right and bottom.
verbose	Print messages
time.resolve	Activate to stop R from loading raw images into memory

Value

A Staffli object

A Seurat object

Examples

## Not run: 
# Create a new Staffli object and plot images
st.obj <- CreateStaffliObject(imgs, meta.data)
st.obj <- LoadImages(st.obj, verbose = TRUE)
plot(st.obj)

## End(Not run)

## Not run: 
# Load images into a Seurat object and plot images
se <- LoadImages(se, verbose = TRUE)
ImagePlot(se)

## End(Not run)

jbergenstrahle/STUtility documentation built on March 14, 2023, 7:15 a.m.