annotate_foci_counting {synapsis}R Documentation

annotate_foci_counting

Description

Contains all plotting routines for count foci annotation

Usage

annotate_foci_counting(
  img_file,
  cell_count,
  img_orig,
  img_orig_foci,
  artificial_amp_factor,
  strands,
  coincident_foci,
  foci_label,
  alone_foci,
  percent_px,
  foci_per_cell
)

Arguments

img_file

cell's file name

cell_count

unique cell counter

img_orig

original strand crop

img_orig_foci

cropped foci channel

artificial_amp_factor

amplification factor

strands

black white mask of strand channel

coincident_foci

mask of overlap between strand and foci channel

foci_label

black and white mask of foci channel

alone_foci

estimated number of foci that are NOT on a strand.

percent_px

percentage of foci mask that coincides with strand channel small number indicates potentially problematic image.

foci_per_cell

number of foci counted per cell

Value

displays key steps from raw image to coincident foci count


[Package synapsis version 0.99.18 Index]