make_strand_mask {synapsis} | R Documentation |
creates strand mask for strand channel crop
make_strand_mask( offset_px, stage, img_orig, disc_size, brush_size, brush_sigma )
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. |
strand mask