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 notSpatialFeatureExperiment
because the spatial extent of images in SFE takes precedence.- value
New version of image to add, must inherit from
VirtualSpatialImage
.
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/Rtmpr2gFdA/file24bf1969321/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
#> >>> 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)