Estimate reconstruction parameters from a set of images

Usage

estimateReconstructionParametersSPE(
  spe,
  marks,
  image_col,
  mark_select = NULL,
  nimages = NULL,
  fun = "bw.diggle",
  dim = 500,
  ncores = 1,
  plot_hist = TRUE
)

Arguments

spe: SpatialExperiment; a object of class SpatialExperiment
marks: character; name of column in colData that will correspond to the ppp marks
image_col: character; name of a column in colData that corresponds to the image
mark_select: character; name of mark that is to be selected for the reconstruction
nimages: integer; number of images for the estimation. Will be randomly sampled
fun: character; function to estimate the kernel density. Default bw.diggle.
dim: numeric; x dimension of the final reconstruction. A lower resolution speed up computation but lead to less exact reconstruction. Default = 500
ncores: numeric; number of cores for parallel processing using mclapply. Default = 1
plot_hist: logical; if histogram of estimated densities and thresholds should be plotted. Default = TRUE

Value

tibble; tibble with estimated intensities and thresholds

Examples

spe <- imcdatasets::Damond_2019_Pancreas("spe", full_dataset = FALSE)
#> see ?imcdatasets and browseVignettes('imcdatasets') for documentation
#> loading from cache
spe_sel <- spe[, spe[["image_name"]] %in% c("E02", "E03", "E04")]
estimateReconstructionParametersSPE(spe_sel,
    marks = "cell_category",
    image_col = "image_name", mark_select = "islet", plot_hist = TRUE
)

#>   img     bndw       thres
#> 1 E02 18.61921 0.004187900
#> 2 E04 11.35910 0.003918334
#> 3 E03 17.85633 0.003913723