annotate_foci_counting {synapsis} | R Documentation |
Contains all plotting routines for count foci annotation
annotate_foci_counting( img_file, cell_count, img_orig, img_orig_foci, artificial_amp_factor, strands, coincident_foci, foci_label, alone_foci, percent_px, foci_per_cell )
img_file |
cell's file name |
cell_count |
unique cell counter |
img_orig |
original strand crop |
img_orig_foci |
cropped foci channel |
artificial_amp_factor |
amplification factor |
strands |
black white mask of strand channel |
coincident_foci |
mask of overlap between strand and foci channel |
foci_label |
black and white mask of foci channel |
alone_foci |
estimated number of foci that are NOT on a strand. |
percent_px |
percentage of foci mask that coincides with strand channel small number indicates potentially problematic image. |
foci_per_cell |
number of foci counted per cell |
displays key steps from raw image to coincident foci count