spots.combined.folder {nucim}

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