get_foci_per_cell {synapsis} | R Documentation |
creates mask for coincident foci
get_foci_per_cell( img_file, offset_px, stage, strands, watershed_stop, foci_label, annotation, cell_count, img_orig, img_orig_foci, artificial_amp_factor, coincident_foci )
img_file |
cell's file name |
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. |
strands |
black white mask of strand channel |
watershed_stop |
Stop default watershed method with "on" |
foci_label |
black and white mask of foci channel |
annotation, |
Choice to output pipeline choices (recommended to knit) |
cell_count |
unique cell counter |
img_orig |
original strand crop |
img_orig_foci |
cropped foci channel |
artificial_amp_factor |
amplification factor |
coincident_foci |
mask of coincident foci |
number of foci per cell