def detect_NCC_pos(nuclei, thickness):
IJ.selectWindow("NCC")
imp = IJ.getImage()
IJ.run("Remove Overlay", "")
IJ.run("Overlay Options...", "stroke=green width=0 fill=green set")
IJ.run("Set Measurements...", "area mean redirect=NCC decimal=3")
pos_idx = []
neg_idx = []
idx = 0
#IJ.log("nuclei :"+str(len(nuclei)))
IJ1.batchMode = True
for idx in nuclei:
#IJ.log("idx: "+str(idx))
ncc_roi = rm.select(idx)
IJ.run("Make Band...", "band=" + str(thickness))
#rm.runCommand("Update")
if IJ.getValue(wm.getImage("NCC"), "Mean") > ncc_threshold:
pos_idx.append(idx)
rm.rename(idx, str(idx) + "-NCC-POS")
IJ.run(imp, "Add Selection...", "")
IJ.run(imp, "Select None", "")
else:
neg_idx.append(idx)
rm.rename(idx, str(idx) + "-NCC-NEG")
IJ1.batchMode = False
IJ.run("Show Overlay", "")
IJ.log("Number of NCC+ cells: " + str(len(pos_idx)))
IJ.log("Number of NCC- cells: " + str(len(neg_idx)))
return pos_idx
def detect_MR_pos(nuclei):
IJ.selectWindow("MR")
IJ.run("Remove Overlay", "")
IJ.run("Overlay Options...", "stroke=red width=0 fill=red set")
IJ.run("Set Measurements...", "area mean redirect=MR decimal=3")
pos_idx = []
neg_idx = []
idx = 0
for idx in nuclei:
rm.select(idx)
MR_mean = IJ.getValue(wm.getImage("MR"), "Mean")
if MR_mean > mr_threshold:
pos_idx.append(idx)
rm.rename(idx, str(idx) + "-MR-POS")
IJ.run(IJ.getImage(), "Add Selection...", "")
else:
neg_idx.append(idx)
rm.rename(idx, str(idx) + "-MR-NEG")
IJ.run("Show Overlay", "")
IJ.log("Number of MR+ cells: " + str(len(pos_idx)))
IJ.log("Number of MR- cells: " + str(len(neg_idx)))
return pos_idx
def filter_nuclei():
area_idx = []
area = 0
stardist_rois = rm.getCount()
IJ.run("Set Measurements...", "area mean redirect=NCC decimal=3")
IJ.selectWindow("Nuclei")
rm.runCommand("Show All without labels")
IJ.selectWindow("NCC")
for nuclei in range(0, stardist_rois):
roi = rm.select(nuclei)
area = IJ.getValue(wm.getImage("NCC"), "Area")
if ((area > min_nucleus_area) and (area < max_nucleus_area)):
area_idx.append(nuclei)
else:
rm.rename(nuclei, str(nuclei) + "-Excluded_(area)")
IJ.log("Number of cells fitting area criteria: " + str(len(area_idx)))
return area_idx
background_auto = 0
# defines the golgi and background at this point.
if man_bck_det is True:
background_auto = low()
else:
background= low()
#try:
# background
#except NameError:
# background = low()
#else:
# background_auto = low()
if mean_max_det is True:
cell_area = IJ.getValue(imp, "Area")
bck_int = []
mean_int = []
maximum_int = []
for channel in channel_iterator:
channel_first = int(channel)
IJ.setSlice(channel_first)
# Data Collection
if man_bck_det is True:
bck_int=man_bck_list
else:
bck_int.append(low()) # background
mean_int.append(selection_mean())
maximum_int.append(high(bit_depth))
IJ.run("Select None")
to_transport_channel()