Commit 01d0a9f0 authored by Lucy McNeill's avatar Lucy McNeill
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count_foci function outputs display when run with annotate = on

parent 87eb1899
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......@@ -135,18 +135,18 @@ count_foci <- function(img_path, stage = "none", offset_px = 0.2, offset_factor
print("cell counter is")
print(cell_count)
print("original images")
display(new_img)
display(img_orig_foci)
plot(new_img)
plot(img_orig_foci)
print("displaying resulting foci count")
print("Overlay two channels")
display(rgbImage(strands,foci_label,0*foci_label))
plot(rgbImage(strands,foci_label,0*foci_label))
#print("showing the watershed masks")
#display(foci_th)
#display(colorLabels(watershed(bwlabel(foci_th)*as.matrix(img_orig_foci),tolerance=0.05, ext=1)))
print("coincident foci")
display(colorLabels(coincident_foci))
plot(colorLabels(coincident_foci))
print("two channels, only coincident foci")
display(rgbImage(strands,coincident_foci,coincident_foci))
plot(rgbImage(strands,coincident_foci,coincident_foci))
}
overlap_no = table(coincident_foci)
......@@ -181,7 +181,7 @@ count_foci <- function(img_path, stage = "none", offset_px = 0.2, offset_factor
print(alone_foci)
if(alone_foci < 0){
print("this one had a negative lone foci amount. Suspect overcounting of foci in this one:")
display(rgbImage(strands,foci_label,0*foci_label))
plot(rgbImage(strands,foci_label,0*foci_label))
}
}
percent_px <- sum(overlap)/sum(foci_areas)
......
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