find.spots.file {nucim}

Detects spots for one file

Description

Detects spots for one file

Usage

find.spots.file(
  file,
  dir,
  color,
  thresh = NULL,
  thresh.auto = FALSE,
  thresh.quantile = 0.9,
  filter = NULL,
  cores = 1
)

Arguments

file

file

dir

directory for results

color

which color, images have to be in folder with color name

thresh

threshold

thresh.auto

Logical. Find threshold automatically?

thresh.quantile

numeric. use simple

filter

2d-filter to use before spot detection

cores

number of cores to use in parallel (with parallel package only)

Value

spot images in spot-color/, number of spots as txt files in spot-color/