def analyzeTUB():
rm = RoiManager().getInstance()
#Set imageJ preference meassurements to "area"
IJ.run("Set Measurements...", "area display redirect=None decimal=3")
#Variable used for iteration
counter = 0
#Clear previous resuslts
IJ.run("Clear Results")
# Make library, to be iterated through. Room for improvement
lis_dic = [{'path': sub[i]} for i in range(len(sub))]
if not lis_dic:
sys.exit('Did you check the right box?')
# Calculate area of channel #1 (Calculation requires that area is chosen as measured value)
for i in lis_dic:
print i
for p in data[counter][::-1]:
print p
if '_' + channel1 + '_' in p:
imp1 = IJ.openImage(i['path'] + '/' + p)
IJ.setThreshold(imp1, lowth1, 255)
IJ.run(imp1, "Create Selection", "")
roi = rm.getRoi(imp1)
#rm.runCommand(imp1, 'Add')
IJ.run(imp1, "Measure", "")
if '_' + channel2 + '_' in p:
imp2 = IJ.openImage(i['path'] + '/' + p)
IJ.setThreshold(imp2, lowth2, 255)
rm.runCommand(imp1, 'Select')
IJ.run(imp2, "Analyze Particles...", "size=0-4000 summarize")
counter += 1
# Reset counter
counter = 0
IJ.renameResults(channel2)
def analyzeDAPI():
#Set imageJ preference meassurements to "area"
IJ.run("Set Measurements...", "area display redirect=None decimal=3")
#Variable used for iteration
counter = 0
#Clear previous resuslts
IJ.run("Clear Results")
# Make library, to be iterated through. Room for improvement
lis_dic = [{'path': sub[i]} for i in range(len(sub))]
if not lis_dic:
sys.exit('Did you check the right box?')
# Calculate number of particles in channel #1 (Calculation requires that DAPI is chosen as measured value)
for i in lis_dic:
for p in data[counter]:
if '_' + channel1 + '_' in p:
imp1 = IJ.openImage(i['path'] + '/' + p)
IJ.setThreshold(imp1, lowth1, 255)
IJ.run(imp1, "Convert to Mask", "")
IJ.run(imp1, "Watershed", "")
IJ.run(imp1, "Analyze Particles...",
"size=200-3000 pixel summarize")
counter += 1
IJ.renameResults(channel1)
# Reset counter
counter = 0
# Calculate area of channel #2
for i in lis_dic:
for p in data[counter]:
if '_' + channel2 + '_' in p:
imp2 = IJ.openImage(i['path'] + '/' + p)
IJ.setThreshold(imp2, lowth2, 255)
IJ.run(imp2, "Create Selection", "")
IJ.run(imp2, "Measure", "")
counter += 1
IJ.renameResults(channel2)
for jj in range(0, 65536):
ii += hist[jj]
if ii > histsum / 2:
break
return jj
gd = GenericDialog("Image Information")
gd.addNumericField("Cardiomyocye Stain Channel Number", 1, 0, 10, "")
gd.addNumericField("Nuclear Stain Channel Number", 2, 0, 10, "")
gd.showDialog()
cmChan = int(gd.getNextNumber())
nucChan = int(gd.getNextNumber())
IJ.setProperty("cmChan", cmChan)
IJ.setProperty("nucChan", nucChan)
analyte = WindowManager.getCurrentImage()
title = analyte.getTitle()
IJ.run("Split Channels")
nucTitle = "C{}-{}".format(nucChan, title)
nucIp = WindowManager.getImage(nucTitle)
nucIpMedian = calcMedian(nucIp)
IJ.run(nucIp, "Subtract...", "value=" + str(nucIpMedian) + " stack")
IJ.run("Merge Channels...",
"c1=[C1-{}] c2=[C2-{}] create".format(title, title))
cmt = ResultsTable()
cmt.show("Cardiomyocyte Results")
IJ.renameResults("Cardiomyocyte Results")
nuct = ResultsTable()
nuct.show("Nucleus Results")
IJ.renameResults("Nucleus Results")