make_foci_mask {synapsis} | R Documentation |
creates foci mask for foci channel crop
make_foci_mask( offset_factor, bg, crowded_foci, img_orig_foci, brush_size, brush_sigma, disc_size_foci )
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 |
foci mask