nucim (version 1.0.11)

spots.combined: Find spots using information from two channels

Description

Find spots using information from two channels

Usage

spots.combined(
  red,
  green,
  mask,
  size = NULL,
  voxelsize = NULL,
  thresh.offset = 0.1,
  window = c(5, 5),
  min.sum.intensity = 2,
  max.distance = 0.5,
  use.brightest = FALSE,
  max.spots = NA,
  full.voxel = FALSE
)

Arguments

red

image

green

image

mask

image mask

size

size of img in microns

voxelsize

size of voxel in microns

thresh.offset

Thresh offset used in EBImage::thresh()

window

Half width and height of the moving rectangular window.

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

Value

RGB image with spots will be written to output folder