Find spots based on threshold and minimum total intensity

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.

array