get_foci_per_cell: get_foci_per_cell

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

Description

creates mask for coincident foci

Usage

get_foci_per_cell(
  img_file,
  offset_px,
  stage,
  strands,
  watershed_stop,
  foci_label,
  annotation,
  cell_count,
  img_orig,
  img_orig_foci,
  artificial_amp_factor,
  coincident_foci
)

Arguments

img_file	cell's file name
offset_px,	Pixel value offset used in thresholding of synaptonemal complex channel
stage,	meiosis stage of interest. Currently count_foci determines this with thresholding/ object properties in the synaptonemal complex channel by previosly calling the get_pachytene function. Note that if using this option, the count_foci function requires that the input directory contains a folder called “pachytene” with the crops in it.
strands	black white mask of strand channel
watershed_stop	Stop default watershed method with "on"
foci_label	black and white mask of foci channel
annotation,	Choice to output pipeline choices (recommended to knit)
cell_count	unique cell counter
img_orig	original strand crop
img_orig_foci	cropped foci channel
artificial_amp_factor	amplification factor
coincident_foci	mask of coincident foci

Value

number of foci per cell

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