spots.combined.file {nucim}

Find spots using information from two channels

Description

Find spots using information from two channels

Usage

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

Arguments

file

File name

size

size of img in microns, if size and voxelsize are NULL, size is determined from folder XYZmic

voxelsize

size of voxel in microns

folder

Folder

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

Value

RGB image with spots will be written to output folder