Image setter

Modify or replace images stored in a SpatialExperiment object. This is different from addImg which adds the image from files and can't replace existing images, which is there to be consistent with SpatialExperiment. This setter here can replace existing images with another object that inherits from VirtualSpatialImage, including SpatRasterImage, BioFormatsImage, and ExtImage.

Usage

# S4 method for class 'SpatialExperiment'
Img(x, sample_id = 1L, image_id, scale_fct = 1) <- value

Arguments

x

A SpatialExperiment object, which includes SFE.

sample_id

Which sample the image is associated with. Use sampleIDs to get sample IDs present in the SFE object.

image_id

Image ID, such as "lowres" and "hires" for Visium data and "DAPI" and "PolyT" for Vizgen MERFISH data.

scale_fct

Scale factor to convert pixels in lower resolution to those in the full resolution. Only relevant to image classes implemented in SpatialExperiment but not SpatialFeatureExperiment because the spatial extent of images in SFE takes precedence.

value

New version of image to add, must inherit from VirtualSpatialImage.

Value

SFE object with the new image added.

Examples

library(EBImage)
#> 
#> Attaching package: ‘EBImage’
#> The following objects are masked from ‘package:SpatialFeatureExperiment’:
#> 
#>     affine, rotate, translate, transpose
library(SFEData)
library(RBioFormats)
#> BioFormats library version 7.3.0
fp <- tempfile()
fn <- XeniumOutput("v2", file_path = fp)
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
#> The downloaded files are in /tmp/RtmpUGEtoo/file834d40c00e8a/xenium2 
# Weirdly the first time I get the null pointer error
try(sfe <- readXenium(fn))
#> >>> Cell segmentations are found in `.parquet` file(s)
#> >>> Reading cell and nucleus segmentations
#> >>> Making MULTIPOLYGON nuclei geometries
#> >>> Making POLYGON cell geometries
#> Sanity checks on cell segmentation polygons:
#> >>> ..found 132 cells with (nested) polygon lists
#> >>> ..applying filtering
#> >>> Checking polygon validity
#> >>> Saving geometries to parquet files
#> >>> Reading cell metadata -> `cells.parquet`
#> >>> Reading h5 gene count matrix
#> >>> filtering cellSeg geometries to match 6272 cells with counts > 0
#> >>> filtering nucSeg geometries to match 6158 cells with counts > 0
sfe <- readXenium(fn)
#> >>> Preprocessed sf segmentations found
#> >>> Reading cell and nucleus segmentations
#> >>> Reading cell metadata -> `cells.parquet`
#> >>> Reading h5 gene count matrix
#> >>> filtering cellSeg geometries to match 6272 cells with counts > 0
#> >>> filtering nucSeg geometries to match 6158 cells with counts > 0
img <- getImg(sfe) |> toExtImage(resolution = 1L)
img <- img[,,1] > 500
Img(sfe, image_id = "mask") <- img
imageIDs(sfe)
#> [1] "morphology_focus" "mask"            
unlink(fn, recursive = TRUE)