make_foci_mask {synapsis}R Documentation

make_foci_mask

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


[Package synapsis version 0.99.18 Index]