Reconstruct structure from spatial experiment object per image id

Usage

reconstructShapeDensitySPE(
  spe,
  marks,
  imageCol,
  markSelect,
  dim = 500,
  bndw = NULL,
  thres = NULL,
  nCores = 1
)

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
dim: numeric; x dimension of the final reconstruction. A lower resolution speed up computation but lead to less exact reconstruction. Default = 500
bndw: numeric; bandwidth of the sigma parameter in the density estimation, if no value is given the bandwidth is estimated using cross validation with the bw.diggle function for each image individually.
thres: numeric; intensity threshold for the reconstruction; if NULL the threshold is set as the mean between the mode of the pixel intensity distributions estimated for each image individual
nCores: numeric; number of cores for parallel processing using mclapply. Default = 1

Value

simple feature collection

Examples

data("sostaSPE")
allStructs <- reconstructShapeDensitySPE(sostaSPE,
    marks = "cellType", imageCol = "imageName",
    markSelect = "A", bndw = 3.5, thres = 0.005
)
allStructs
#> Simple feature collection with 5 features and 2 fields
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: 0.003206789 ymin: 0.01876509 xmax: 127.9648 ymax: 127.9749
#> CRS:           NA
#>          structID imageName                   sostaPolygon
#> image1   image1_1    image1 POLYGON ((52.22127 127.9601...
#> image2.1 image2_1    image2 POLYGON ((0.5238102 13.0702...
#> image2.2 image2_2    image2 POLYGON ((12.29547 127.719,...
#> image2.3 image2_3    image2 POLYGON ((52.47265 127.4631...
#> image3   image3_1    image3 POLYGON ((25.3302 127.8568,...