annotate_foci_counting: annotate_foci_counting

In mcneilllucy/synapsis: An R package to automate the analysis of double-strand break repair during meiosis

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

mcneilllucy/synapsis documentation built on Dec. 21, 2021, 3:59 p.m.