spots {bioimagetools}

Find spots based on threshold and minimum total intensity

Description

Find spots based on threshold and minimum total intensity

Usage

spots(
  img,
  mask,
  thresh.offset = 0.1,
  window = c(5, 5),
  min.sum.intensity = 0,
  zero = NA,
  max.spots = NULL,
  return = "intensity"
)

Arguments

img

image array.

mask

mask array.

thresh.offset

threshold for minimum voxel intensity.

window

Half width and height of the moving rectangular window.

min.sum.intensity

threshold for minimum total spot intensity

zero

if NA, background is set to NA, if 0, background is set to 0.

max.spots

find max.spots spots with highest total intensity.

return

"mask" returns binarized mask, "intensity" returns intensity for spots, zero or NA otherwise "label" return labeled (numbered) spots.

Value

array