CropImages: Manual cropping of images

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

Manual cropping of images

Description

Takes a predefined list of crop windows and cuts each image

Usage

CropImages(
  object,
  crop.geometry.list,
  xdim = NULL,
  time.resolve = FALSE,
  verbose = FALSE,
  ...
)

## S3 method for class 'Staffli'
CropImages(
  object,
  crop.geometry.list,
  xdim = NULL,
  time.resolve = FALSE,
  verbose = FALSE,
  ...
)

## S3 method for class 'Seurat'
CropImages(
  object,
  crop.geometry.list,
  xdim = NULL,
  time.resolve = FALSE,
  verbose = FALSE,
  ...
)

Arguments

object	Seurat object
crop.geometry.list	List of crop windows. Each element of the list should be named by a section number that the cropping should be applied to, e.g. "1", "2", "3", etc. The crop window is defined by a string speficying the size of the output window and the offset in pixels; "_width_x_height_+_offsetx_+_offsety_". Note that the cropping will be applied to the original HE images, i.e. the images that were loaded when running 'LoadImages'. See details below for more information.
xdim	Maximum width of cropped window
time.resolve	Activate to stop R from loading raw images into memory
verbose	Print messages
...	Additional parameters

Details

Let's say that you want to crop out a smaller piece of secttion 1 that should be 500x500 pixels and should be offset by 400 pixels along the x axis and 400 pixels along the y axis. The y axis starts from the top of the image so the offset will essentially determine the top left corner of the output cropped image. To do this, you can set 'crop.geometry.list = list("1" = "500x500+400+400")'. If 'xdim' is not specified, the function will collect the predefined 'xdim' that was set when running 'LoadImages'. The 'xdim' value determines the maximum allowed width of the cropped image, so if you for example set a large crop window from the original image, e.g. "2000x2000+1000+1000" the output image will still be downscaled to a width of 'xdim' to keep the output image in low resolution.

Value

A Staffli object

A Seurat object

Examples

## Not run: 
# Load images
st.object <- GetStaffli(se)

# Crop section 1 to a size of 500x500 pixels offset by (500, 500) pixels from the top left corner
st.object<- CropImages(st.object, crop.geometry.list = list("1" = "500x500+500+500"))

## End(Not run)
## Not run: 
# Load images
se <- LoadImages(se)

# Crop section 1 to a size of 500x500 pixels offset by (500, 500) pixels from the top left corner
se <- CropImages(se, crop.geometry.list = list("1" = "500x500+500+500"))

## End(Not run)

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