Estimate reconstruction parameters from a set of images

Usage

estimateReconstructionParametersSPE(
  spe,
  marks,
  imageCol,
  markSelect = NULL,
  nImages = NULL,
  fun = "bw.diggle",
  dim = 500,
  nCores = 1,
  plotHist = TRUE
)

Arguments

spe: SpatialExperiment; a object of class SpatialExperiment
marks: character; name of column in colData that will correspond to the ppp marks
imageCol: character; name of a column in colData that corresponds to the image
markSelect: 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
plotHist: logical; if histogram of estimated densities and thresholds should be plotted. Default = TRUE

Value

tibble; tibble with estimated intensities and thresholds

Examples

data("sostaSPE")
estimateReconstructionParametersSPE(sostaSPE,
    marks = "cellType", imageCol = "imageName",
    markSelect = "A", plotHist = TRUE
)

#>                 img     bndw      thres
#> image1 c(113.96.... 3.655770 0.04424890
#> image2 c(84.159.... 3.568156 0.05912054
#> image3 c(29.747.... 4.189788 0.03065195