Find spots using information from two channels for folder

Usage

spots.combined.folder(
  path,
  size = NULL,
  voxelsize = NULL,
  thresh.offset = 0.1,
  min.sum.intensity = 2,
  max.distance = 0.5,
  use.brightest = FALSE,
  max.spots = 2,
  full.voxel = FALSE,
  output = "markers",
  cores = 1
)

Arguments

path: path to folder
size: size of img in microns, if size and voxelsize are NULL, size is determined from folder XYZmic
voxelsize: size of voxel in microns
thresh.offset: Thresh offset used in EBImage::thresh()
min.sum.intensity: spots smaller than min.sum.intensity are ignored
max.distance: use only spots with distance to other color spot smaller than max.distance
use.brightest: Logical; use only brightest in max.distance?
max.spots: maximum of spots (per channel), only when use brightest=TRUE
full.voxel: Logical; output contains full voxel instead of rgb intensities
output: output folder
cores: number of cores we can use of parallel computing (needs parallel package if cores>1)

Value

RGB image with spots will be written to output folder