def threshold(imPlus, edgeThreshold=2500):
mask = Duplicator().run(imPlus)
mask_stk = mask.getStack()
# First, we threshold based on edges
IJ.setThreshold(mask, edgeThreshold, 100000, "No Update")
for i in range(mask.getImageStackSize()):
mask_stk.getProcessor(i + 1).findEdges()
IJ.run(mask, "Make Binary", "method=Default background=Default black")
# Now, we need to clean up the binary images morphologically
IJ.run(mask, "Dilate", "stack")
IJ.run(mask, "Fill Holes", "stack")
IJ.run(mask, "Erode", "stack")
IJ.run(mask, "Erode", "stack")
# Finally, remove the small particles
stk = ImageStack(mask.getWidth(), mask.getHeight())
p = PA(PA.SHOW_MASKS, 0, None, 200, 100000)
p.setHideOutputImage(True)
for i in range(mask_stk.getSize()):
mask.setSliceWithoutUpdate(i + 1)
p.analyze(mask)
mmap = p.getOutputImage()
stk.addSlice(mmap.getProcessor())
mask.setStack(stk)
mask.setSliceWithoutUpdate(1)
mask.setTitle(mask_title(imPlus.getTitle()))
mask.show()
return mask
def segmentNuc(impc2):
impdup = Duplicator().run(impc2)
IJ.run(impdup, "8-bit", "")
IJ.run(impdup, "Gaussian Blur...", "sigma=1.5 stack")
# AutoThresholder().getThreshold(AutoThresholder.Method.valuOf('Otsu'), int[] histogram)
IJ.setAutoThreshold(impdup, "Otsu dark")
IJ.run(impdup, "Convert to Mask", "stack")
#IJ.setAutoThreshold(impdup, "Otsu dark")
#opt = PA.SHOW_MASKS + PA.SHOW_RESULTS + PA.EXCLUDE_EDGE_PARTICLES + PA.INCLUDE_HOLES # option for stack missing
opt = PA.SHOW_MASKS + PA.EXCLUDE_EDGE_PARTICLES + PA.INCLUDE_HOLES # option for stack missing
##area mean centroid bounding integrated stack redirect=None decimal=4
meas = Meas.AREA + Meas.MEAN + Meas.CENTROID + Meas.RECT + Meas.INTEGRATED_DENSITY + Meas.STACK_POSITION
rt = ResultsTable().getResultsTable()
pa = PA(opt, meas, rt, 10.0, 300000.0, 0, 1.0)
PA.processStack = True
pa.setHideOutputImage(True)
##run("Analyze Particles...", "size=800-Infinity circularity=0.00-1.00 pixel show=Masks display exclude include stack");
outstack = ImageStack(impdup.getWidth(), impdup.getHeight())
for i in range(1,impdup.getStackSize()+1):
impdup.setSlice(i)
pa.analyze(impdup)
impbin = pa.getOutputImage()
outstack.addSlice(impbin.getProcessor())
impbin = ImagePlus("out", outstack)
IJ.run(impbin, "Invert LUT", "")
#IJ.run(impbin, "Fill Holes", "stack")
return impbin, rt
def analyze(imp, min_area):
MAXSIZE = 1000000000000
MINCIRCULARITY = 0.0
MAXCIRCULARITY = 1.
options = PA.SHOW_MASKS
temp_results = ResultsTable()
p = PA(options, PA.AREA + PA.MEAN, temp_results, min_area, MAXSIZE, MINCIRCULARITY, MAXCIRCULARITY)
p.setHideOutputImage(True)
p.analyze(imp)
if temp_results.getCounter() == 0:
areas = []
signals = []
else:
areas = list(temp_results.getColumn(0))
signals = list(temp_results.getColumn(1))
count = len(areas)
area = sum(areas)
total = 0
if area > 0:
total = sum([a*s for a,s in zip(areas, signals)]) / area
return p.getOutputImage(), count, area, total
def analyzeParticles(imp, minsize, maxsize, mincirc, maxcirc,
filename='Test.czi',
addROIManager=True,
headless=True,
exclude=True):
if addROIManager is True:
if exclude is False:
options = PA.SHOW_ROI_MASKS \
+ PA.SHOW_RESULTS \
+ PA.DISPLAY_SUMMARY \
+ PA.ADD_TO_MANAGER \
+ PA.ADD_TO_OVERLAY \
if exclude is True:
options = PA.SHOW_ROI_MASKS \
+ PA.SHOW_RESULTS \
+ PA.DISPLAY_SUMMARY \
+ PA.ADD_TO_MANAGER \
+ PA.ADD_TO_OVERLAY \
+ PA.EXCLUDE_EDGE_PARTICLES
if addROIManager is False:
if exclude is False:
options = PA.SHOW_ROI_MASKS \
+ PA.SHOW_RESULTS \
+ PA.DISPLAY_SUMMARY \
+ PA.ADD_TO_OVERLAY \
if exclude is True:
options = PA.SHOW_ROI_MASKS \
+ PA.SHOW_RESULTS \
+ PA.DISPLAY_SUMMARY \
+ PA.ADD_TO_OVERLAY \
+ PA.EXCLUDE_EDGE_PARTICLES
measurements = PA.STACK_POSITION \
+ PA.LABELS \
+ PA.AREA \
+ PA.RECT \
results = ResultsTable()
p = PA(options, measurements, results, minsize, maxsize, mincirc, maxcirc)
p.setHideOutputImage(True)
particlestack = ImageStack(imp.getWidth(), imp.getHeight())
for i in range(imp.getStackSize()):
imp.setSliceWithoutUpdate(i + 1)
ip = imp.getProcessor()
#IJ.run(imp, "Convert to Mask", "")
p.analyze(imp, ip)
mmap = p.getOutputImage()
particlestack.addSlice(mmap.getProcessor())
return particlestack, results
def removeSmallCCs(image):
MINSIZE = 1000
MAXSIZE = 1000000
options = PA.SHOW_ROI_MASKS
results = ResultsTable()
p = PA(options, PA.STACK_POSITION + PA.LABELS + PA.AREA + PA.PERIMETER + PA.CIRCULARITY, results, MINSIZE, MAXSIZE)
p.setHideOutputImage(True)
p.analyze(image)
mmap = p.getOutputImage()
mip = mmap.getProcessor()
mip.threshold(0)
img = ImagePlus("rods_processed", mip)
IJ.run(img, "8-bit", "")
IJ.run(img, "Make Binary", "method=Default background=Dark black")
return img
def analyzeParticles(imp,
minsize,
maxsize,
mincirc,
maxcirc,
#filename='Test.czi',
addROIManager=False,
#headless=False,
exclude=True):
if GraphicsEnvironment.isHeadless():
print('Headless Mode detected. Do not use ROI Manager.')
addROIManager = False
if addROIManager:
# get the ROI manager instance
rm = RoiManager.getInstance()
if rm is None:
rm = RoiManager()
rm.runCommand("Associate", "true")
if not exclude:
options = PA.SHOW_ROI_MASKS \
+ PA.SHOW_RESULTS \
+ PA.DISPLAY_SUMMARY \
+ PA.ADD_TO_MANAGER \
+ PA.ADD_TO_OVERLAY \
if exclude:
options = PA.SHOW_ROI_MASKS \
+ PA.SHOW_RESULTS \
+ PA.DISPLAY_SUMMARY \
+ PA.ADD_TO_MANAGER \
+ PA.ADD_TO_OVERLAY \
+ PA.EXCLUDE_EDGE_PARTICLES
if not addROIManager:
if not exclude:
options = PA.SHOW_ROI_MASKS \
+ PA.SHOW_RESULTS \
+ PA.DISPLAY_SUMMARY \
+ PA.ADD_TO_OVERLAY \
if exclude:
options = PA.SHOW_ROI_MASKS \
+ PA.SHOW_RESULTS \
+ PA.DISPLAY_SUMMARY \
+ PA.ADD_TO_OVERLAY \
+ PA.EXCLUDE_EDGE_PARTICLES
measurements = PA.STACK_POSITION \
+ PA.LABELS \
+ PA.AREA \
+ PA.RECT \
+ PA.PERIMETER \
+ PA.SLICE \
+ PA.SHAPE_DESCRIPTORS \
+ PA.CENTER_OF_MASS \
+ PA.CENTROID
results = ResultsTable()
p = PA(options, measurements, results, minsize, maxsize, mincirc, maxcirc)
p.setHideOutputImage(True)
particlestack = ImageStack(imp.getWidth(), imp.getHeight())
for i in range(imp.getStackSize()):
imp.setSliceWithoutUpdate(i + 1)
ip = imp.getProcessor()
# convert to a mask for the particle analyzer
ip.invert()
# do the particle analysis
p.analyze(imp, ip)
mmap = p.getOutputImage()
# add the slide to the full stack
particlestack.addSlice(mmap.getProcessor())
return particlestack, results
def __calRois(self, imp, indice) :
"""
Returns the ROIs of a slice given (identified with its n°) in a stack
"""
##imp=self.__dictImages[nameimages] # IL FAUT RÉCUPÉRER L'IMAGE DU STACK !!!!!
#if self.__batch : imp.hide()
#else : imp.show()
#imp.hide()
imp.show()
if self.__batch : imp.hide()
imp.setSlice(indice)
imp.killRoi()
ip = imp.getProcessor()
bs=BackgroundSubtracter()
#if str(self.__subback) == "0" or str(self.__subback) == "1" : self.__subback = bool(int(self.__subback))
#if self.__subback == True : IJ.run(imp, "Subtract Background...", "rolling="+str(self.__radius)+" light")
if self.__subback == True : bs.rollingBallBackground(ip, self.__radius, False, True, False, True, False)
if self.__runmacro :
imp.show()
imp.setSlice(indice)
imp.updateAndDraw()
IJ.runMacroFile(self.__macropath, imp.getTitle())
imp.updateAndDraw()
#if str(self.__manthresh) == "0" or str(self.__manthresh) == "1" : self.__manthresh = bool(int(self.__manthresh))
#if self.__manthresh : IJ.setThreshold(imp, self.__minthr, self.__maxthr)
if self.__manthresh :
ip.setThreshold(self.__minthr, self.__maxthr, ImageProcessor.RED_LUT)
else : self.__setThreshold(imp, indice)
rt=ResultsTable()
pa1=ParticleAnalyzer(ParticleAnalyzer.SHOW_MASKS+ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES , Measurements.AREA, rt, self.__minArea, self.__maxArea, self.__minCirc, self.__maxCirc)
pa1.setHideOutputImage(True)
pa1.analyze(imp)
masks=pa1.getOutputImage()
masks.getProcessor().erode()
masks.getProcessor().dilate()
masks.getProcessor().invertLut()
masks.getProcessor().threshold(1)
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
rm.runCommand("reset")
#rm.hide()
pa2=ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER+ParticleAnalyzer.CLEAR_WORKSHEET+ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES , Measurements.AREA, rt, self.__minArea, self.__maxArea, self.__minCirc, self.__maxCirc)
pa2.analyze(masks)
masks.close()
temparray=rm.getRoisAsArray()
for r in temparray :
tempnameroi=r.getName()
r.setPosition(indice)
r.setName(str(indice)+"-"+tempnameroi)
r.setStrokeWidth(1)
if len(self.__params) > 0 :
for k in self.__params:
#if k[0]=="Area": self.__minArea, self.__maxArea = str(k[1]), str(k[2])
if k[0]=="Area": self.__minArea, self.__maxArea = k[1], k[2]
for k in self.__params:
#if k[0]=="Circ": self.__minCirc, self.__maxCirc = str(k[1]), str(k[2])
if (k[0]=="Circ") and k[3] : self.__minCirc, self.__maxCirc = k[1], k[2]
else : self.__minCirc, self.__maxCirc = 0, 1
self.__rr.setRoisarray(temparray, imp)
self.__rr.setRange(indice, self.__params)
return self.__rr.includeRois
else : return temparray
# 1. options (could be SHOW_ROI_MASKS, SHOW_OUTLINES, SHOW_MASKS, SHOW_NONE, ADD_TO_MANAGER, and others; combined with bitwise-or)
# 2. measurement options (see [http://imagej.net/developer/api/ij/measure/Measurements.html Measurements])
# 3. a ResultsTable to store the measurements
# 4. The minimum size of a particle to consider for measurement
# 5. The maximum size (idem)
# 6. The minimum circularity of a particle
# 7. The maximum circularity
minSize = 30.0
maxSize = 10000.0
opts = ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES | ParticleAnalyzer.SHOW_OVERLAY_OUTLINES
print(opts)
meas = Measurements.AREA | Measurements.MEAN | Measurements.CENTER_OF_MASS
print(meas)
pa = ParticleAnalyzer(opts, meas, results_table, minSize, maxSize)
# pa.setHideOutputImage(False)
pa.setRoiManager(roim)
if pa.analyze(imp_work):
imp_out = pa.getOutputImage()
# imp_out.show()
roim.runCommand(blobs, "Show All with labels")
blobs.show()
results_table.show("Results")
roim.show()
print "All ok"
else:
print "There was a problem in analyzing", blobs
# The measured areas are listed in the first column of the results table, as a float array:
areas = results_table.getColumn(0)
def nucleusSegmentation(imp2):
""" Segmentation of nucleus image.
Nucleus are selected that:
1. No overlapping with dilated regions
2. close to circular shape. Deformed nuclei are rejected.
Outputs a binary image.
"""
#Convert to 8bit
ImageConverter(imp2).convertToGray8()
#blur slightly using Gaussian Blur
radius = 2.0
accuracy = 0.01
GaussianBlur().blurGaussian( imp2.getProcessor(), radius, radius, accuracy)
# Auto Local Thresholding
imps = ALT().exec(imp2, "Bernsen", 15, 0, 0, True)
imp2 = imps[0]
#ParticleAnalysis 0: prefiltering by size and circularity
rt = ResultsTable()
paOpt = PA.CLEAR_WORKSHEET +\
PA.SHOW_MASKS +\
PA.EXCLUDE_EDGE_PARTICLES +\
PA.INCLUDE_HOLES #+ \
# PA.SHOW_RESULTS
measOpt = PA.AREA + PA.STD_DEV + PA.SHAPE_DESCRIPTORS + PA.INTEGRATED_DENSITY
MINSIZE = 20
MAXSIZE = 10000
pa0 = PA(paOpt, measOpt, rt, MINSIZE, MAXSIZE, 0.8, 1.0)
pa0.setHideOutputImage(True)
pa0.analyze(imp2)
imp2 = pa0.getOutputImage() # Overwrite
imp2.getProcessor().invertLut()
#impNuc = imp2.duplicate() ## for the ring.
impNuc = Duplicator().run(imp2)
#Dilate the Nucleus Area
## this should be 40 pixels in Cihan's method, but should be smaller.
#for i in range(20):
# IJ.run(imp2, "Dilate", "")
rf = RankFilters()
rf.rank(imp2.getProcessor(), RIMSIZE, RankFilters.MAX)
#Particle Analysis 1: get distribution of sizes.
paOpt = PA.CLEAR_WORKSHEET +\
PA.SHOW_NONE +\
PA.EXCLUDE_EDGE_PARTICLES +\
PA.INCLUDE_HOLES #+ \
# PA.SHOW_RESULTS
measOpt = PA.AREA + PA.STD_DEV + PA.SHAPE_DESCRIPTORS + PA.INTEGRATED_DENSITY
rt1 = ResultsTable()
MINSIZE = 20
MAXSIZE = 10000
pa = PA(paOpt, measOpt, rt1, MINSIZE, MAXSIZE)
pa.analyze(imp2)
#rt.show('after PA 1')
#particle Analysis 2: filter nucleus by size and circularity.
#print rt1.getHeadings()
if (rt1.getColumnIndex('Area') > -1):
q1, q3, outlier_offset = getOutlierBound(rt1)
else:
q1 = MINSIZE
q3 = MAXSIZE
outlier_offset = 0
print imp2.getTitle(), ": no Nucleus segmented,probably too many overlaps"
paOpt = PA.CLEAR_WORKSHEET +\
PA.SHOW_MASKS +\
PA.EXCLUDE_EDGE_PARTICLES +\
PA.INCLUDE_HOLES #+ \
# PA.SHOW_RESULTS
rt2 = ResultsTable()
#pa = PA(paOpt, measOpt, rt, q1-outlier_offset, q3+outlier_offset, circq1-circoutlier_offset, circq3+circoutlier_offset)
pa = PA(paOpt, measOpt, rt2, q1-outlier_offset, q3+outlier_offset, 0.8, 1.0)
pa.setHideOutputImage(True)
pa.analyze(imp2)
impDilatedNuc = pa.getOutputImage()
#filter original nucleus
filteredNuc = ImageCalculator().run("AND create", impDilatedNuc, impNuc)
return filteredNuc
