Method to extract image scale factors

Usage

GetScaleFactors(object)

# S4 method for Staffli
GetScaleFactors(object)

# S4 method for Seurat
GetScaleFactors(object)

Arguments

object: A Staffli or Seurat object

Value

A tbl with image scale factors

Examples


# Load example data
se_mbrain <- readRDS(system.file("extdata/mousebrain", "se_mbrain", package = "semla")) |> 
   LoadImages()
#> 
#> ── Loading H&E images ──
#> 
#> ℹ Loading image from /private/var/folders/z8/nrcst881607gn95xh3_4qvb00000gp/T/Rtmpf80zo9/temp_libpath1c4b5544360a/semla/extdata/mousebrain/spatial/tissue_lowres_image.jpg
#> ℹ Scaled image from 600x565 to 400x377 pixels
#> ℹ Saving loaded H&E images as 'rasters' in Seurat object

# Fetch Staffli object
staffli_object <- GetStaffli(se_mbrain)

# Fetch images from a Staffli object
scalefactors <- GetScaleFactors(staffli_object)
scalefactors
#> # A tibble: 1 × 5
#>   spot_diameter_fullres tissue_hires_scalef fiducial_diameter_fullres
#>                   <dbl>               <dbl>                     <dbl>
#> 1                  143.               0.104                      215.
#> # ℹ 2 more variables: tissue_lowres_scalef <dbl>, sampleID <chr>


# Fetch images from a Seurat object
scalefactors <- GetScaleFactors(se_mbrain)
scalefactors
#> # A tibble: 1 × 5
#>   spot_diameter_fullres tissue_hires_scalef fiducial_diameter_fullres
#>                   <dbl>               <dbl>                     <dbl>
#> 1                  143.               0.104                      215.
#> # ℹ 2 more variables: tissue_lowres_scalef <dbl>, sampleID <chr>