make_foci_mask: make_foci_mask

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

Description

creates foci mask for foci channel crop

Usage

make_foci_mask(
  offset_factor,
  bg,
  crowded_foci,
  img_orig_foci,
  brush_size,
  brush_sigma,
  disc_size_foci
)

Arguments

offset_factor	Pixel value offset used in thresholding of foci channel
bg	background value- currently just mean pixel value of whole image
crowded_foci	TRUE or FALSE, defaults to FALSE. Set to TRUE if you have foci > 100 or so.
img_orig_foci	cropped foci channel
brush_size	size of brush to smooth the foci channel. Should be small to avoid erasing foci.
brush_sigma	sigma for Gaussian smooth of foci channel. Should be small to avoid erasing foci.
disc_size_foci	size of disc for local background calculation in foci channel

Value

foci mask

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