spots.combined.folder: Find spots using information from two channels for folder

In bioimaginggroup/nucim: Nucleome Imaging Toolbox

Find spots using information from two channels for folder

Description

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

bioimaginggroup/nucim documentation built on Sept. 6, 2022, 12:15 p.m.