make_strand_mask: make_strand_mask

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

Description

creates strand mask for strand channel crop

Usage

make_strand_mask(
  offset_px,
  stage,
  img_orig,
  disc_size,
  brush_size,
  brush_sigma
)

Arguments

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.
img_orig	original strand crop
disc_size	size of disc for local background calculation in synaptonemal complex 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.

Value

strand mask

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