def calculate_mean_r(imp, ring_rois, centres):
"""calculate the average distance of the cell surface from the vessel axis"""
w = imp.getWidth()
h = imp.getHeight()
rp = FloatProcessor(w, h)
rpix = rp.getPixels()
for lidx, (roi, centre) in enumerate(zip(ring_rois, centres)):
for thetaidx, (x, y) in enumerate(
zip(roi.getPolygon().xpoints,
roi.getPolygon().xpoints)):
rpix[lidx * w + thetaidx] = math.sqrt((x - centre[0])**2 +
(y - centre[1])**2)
rimp = ImagePlus("Radii", rp)
IJ.setAutoThreshold(rimp, "Intermodes light")
bp = rimp.createThresholdMask()
bp.dilate()
bp.erode()
mask_imp = ImagePlus("Mask", bp)
IJ.run(mask_imp, "Create Selection", "")
roi = mask_imp.getRoi()
rimp.setRoi(roi)
mean_r = rimp.getStatistics().mean
rimp.close()
mask_imp.close()
return mean_r
def nuclei_processor(imp_particles, thresh_type, folder, impname,
channel_name):
rm = RoiManager.getInstance()
if not rm:
rm = RoiManager()
rm.reset()
# define a results table
rt = ResultsTable.getResultsTable()
imp_particles.show()
# generate thresholded image for ROI
nuclei = imp_particles.duplicate()
nuclei.show()
IJ.run("Gaussian Blur...", "sigma=3")
IJ.setAutoThreshold(nuclei, thresh_type)
IJ.run("Convert to Mask")
IJ.run("Fill Holes")
# IJ.run("Watershed")
# select thresholded image (to set ROIs)
IJ.run(
"Set Measurements...",
"area mean standard min area_fraction limit display add redirect=[" +
imp_particles.title + "] decimal=3")
IJ.run("Analyze Particles...",
"size=30-Infinity show=Outlines display clear add")
# get the ROI manager and save
rm.runCommand(
"save selected",
os.path.join(folder, impname + '_' + channel_name + "_ROIs.zip"))
def Analyze(imp): IJ.setAutoThreshold(imp, "Otsu Dark stack") IJ.run(imp, "Convert to Mask", "method=MaxEntropy background=Dark calculate black") #IJ.run(imp, "Invert", "stack") #IJ.run(imp, "Despeckle", "stack") IJ.run(imp, "Watershed", "stack") IJ.run(imp, "Analyze Particles...", "size=2-Infinity pixel show=Masks summarize stack")
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 binarize(f):
Prefs.blackBackground = True
imp = IJ.openImage(f)
if imp:
binimp = imp.duplicate()
bs = BackgroundSubtracter()
ip = binimp.getProcessor()
bs.rollingBallBackground(ip, 15, False, False, False, True, True)
IJ.run(binimp, "Unsharp Mask...", "radius=2 mask=0.9")
def smooth(n=1):
for i in range(n):
IJ.run(binimp, "Smooth", "")
smooth(10)
IJ.setAutoThreshold(binimp, "Moments dark")
IJ.run(binimp, "Make Binary", "thresholded remaining")
smooth(12)
IJ.setAutoThreshold(binimp, "Moments white")
IJ.run(binimp, "Make Binary", "thresholded remaining")
IJ.run(binimp, "Erode", "")
IJ.run(binimp, "Dilate", "")
IJ.run(binimp, "Analyze Particles...",
"size=250-Infinity circularity=0.2-1.00 exclude clear add")
binimp.close()
else:
pass
def threshold(imp, lower, upper): duplicate=Duplicator().run(imp) duplicate.getProcessor().resetMinAndMax() IJ.setAutoThreshold(duplicate, "Default dark"); IJ.setThreshold(duplicate, lower, upper) IJ.run(duplicate, "Convert to Mask", ""); return duplicate
def receive_image():
print "recieving an image ....."
the_data=request.data
fh = open("imageToSave.jpg", "wb")
fh.write(the_data)
fh.close()
imp=IJ.openImage("C:/Users/Lynn/Documents/GitHub/server/imageToSave.jpg")
IJ.run(imp,"8-bit","")
IJ.run(imp,"Subtract Background...", "rolling=100 light disable")
IJ.setAutoThreshold(imp,"Default")
IJ.setAutoThreshold(imp,"Triangle")
IJ.setThreshold(imp,0, 237)
#Macro.setOptions("BlackBackground")
IJ.run(imp, "Convert to Mask","")
IJ.run(imp, "Convert to Mask","")
IJ.run(imp, "Make Binary","")
IJ.run(imp,"Fill Holes","")
IJ.run(imp,"Watershed","")
#IJ.run(imp,"Analyze Particles...", "size=2000-20000 display clear summarize add")
IJ.run(imp,"Analyze Particles...", "size=6000-18000 circularity=0.07-0.25 show=[Overlay Outlines] display clear summarize")
imp.show()
FileSaver(imp).saveAsJpeg("C:/Users/Lynn/Documents/GitHub/server/imageToSave3.jpg")
with open("imageToSave3.jpg", "rb") as imageFile:
to_be_sent_str = imageFile.read()
#print imp
test=bytearray(to_be_sent_str)
print "done"
#RoiManager.runCommand("Show All with labels")
#RoiManager.runCommand("Show All")
#return "other"
return test
def binarize_image(imp_in, str_thr, black_bkg):
"""
binarize_image
Parameters
----------
imp_in: ImagePlus
The ImagePlus to binarize
str_thr String
The threshold string. Example: "Default"
black_bkg: Boolean
Whether the background is black (True) or not (False)
Returns
-------
imp_out ImagePlus
The binarized image
"""
imp_out = imp_in.duplicate()
ti = imp.getShortTitle()
imp_out.setTitle(ti + "_bin")
IJ.setAutoThreshold(imp_out, str_thr)
Prefs.blackBackground = black_bkg
IJ.run(imp_out, "Make Binary", "")
IJ.run(imp_out, "Convert to Mask", "")
return (imp_out)
def analyze(imagefile, outdir, size=10000):
"""Opens a file and creates masks."""
masks = []
image = IJ.openImage(imagefile)
imagetitle = image.getTitle().split(".")[0]
# close existing Summary window
rtframe = WindowManager.getFrame("Summary")
if rtframe is not None:
rtframe.close()
# segmentation
IJ.setAutoThreshold(image, "Default dark");
IJ.run(image, "Options...", "iterations=1 count=1 do=Nothing");
#IJ.run(mask, "Convert to Mask", "");
IJ.run(image, "Analyze Particles...", "size=0-"+str(size)+" show=Masks summarize");
masks.append(IJ.getImage())
IJ.run(image, "Analyze Particles...", "size="+str(size)+"-infinity show=Masks summarize");
masks.append(IJ.getImage())
# get ResultsTable object and save it
rt = WindowManager.getFrame("Summary").getTextPanel().getResultsTable()
rtfile = path.join(outdir, str(size)+"Summary_" + imagetitle + ".csv")
rt.save(rtfile)
# create multi-color merged mask
mergedmask = RGBStackMerge.mergeChannels(masks, False)
for m in masks:
m.close()
mergedmask.setTitle(imagetitle + "-mask.tif")
outputfile = path.join(outdir, mergedmask.getTitle())
IJ.saveAs(mergedmask, "TIFF", outputfile)
def resetpressed(event):
self.__ranges.clear()
self.__image=IJ.getImage()
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
rm.runCommand("reset")
self.__image.killRoi()
IJ.setAutoThreshold(self.__image, "MaxEntropy")
rt=ResultsTable()
pa=ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER+ParticleAnalyzer.CLEAR_WORKSHEET , Measurements.AREA+Measurements.ELLIPSE+Measurements.MEAN, rt, 0.00, 10000.00, 0.00, 1.00)
pa.analyze(self.__image)
self.__roisArray=[]
self.__roisArray=rm.getRoisAsArray()
#rm.runCommand("Show All")
#rm.runCommand("Select All")
#rm.runCommand("Set Color", "blue")
IJ.resetThreshold(self.__image)
keys=self.__slidersDict.keys()
for k in keys:
if k.endswith("min"):
self.__slidersDict[k].setValue(0)
self.__slidersDict[k].repaint()
else:
self.__slidersDict[k].setValue(self.__slidersDict[k].getMaximum())
self.__slidersDict[k].repaint()
def ThresholdMaxEntropy(imp0):
"""Thresholds image and returns thresholded image, merge code still quite clumsy but functional"""
imp0 = IJ.getImage()
impthres = imp0.duplicate()
imp01 = ImagePlus("Channel1", ChannelSplitter.getChannel(imp0, 1))
imp02 = ImagePlus("Channel2", ChannelSplitter.getChannel(imp0, 2))
imp001 = imp01.duplicate()
imp002 = imp02.duplicate()
IJ.setAutoThreshold(imp001, "MaxEntropy dark")
IJ.run(imp001, "Convert to Mask", "")
IJ.run(imp001, "Divide...", "value=255")
IJ.setAutoThreshold(imp002, "MaxEntropy dark")
IJ.run(imp002, "Convert to Mask", "")
IJ.run(imp002, "Divide...", "value=255")
ic = ImageCalculator()
imp0001 = ic.run("Multiply create", imp01, imp001)
ic2 = ImageCalculator()
imp0002 = ic2.run("Multiply create", imp02, imp002)
imp0001.copy()
impthres.setC(1)
impthres.paste()
imp0002.copy()
impthres.setC(2)
impthres.paste()
imp01.close()
imp02.close()
imp001.close()
imp002.close()
imp0001.close()
imp0002.close()
return impthres
def Generate_segmented_image(imp, channel):
imp_Threshold_1 = ExtractChannel(imp1, channel)
imp_Threshold_1.setTitle(("Threshold" + "Channel" + str(channel)))
imp_Threshold_1.show()
IJ.run(imp_Threshold_1, "Median...", "radius=1")
IJ.run(imp_Threshold_1, "Subtract Background...", "rolling=50")
IJ.setAutoThreshold(imp_Threshold_1, "Triangle dark")
#Prefs.blackBackground = True;
IJ.run(imp_Threshold_1, "Convert to Mask", "")
return imp_Threshold_1
def Generate_segmented(imp, channel, threshold_method, filtersize):
imp_Threshold_1 = ExtractChannel(imp1, channel)
imp_Threshold_1.setTitle(("Threshold" + "Channel" + str(channel)))
imp_Threshold_1.show()
IJ.run(imp_Threshold_1, "Median...", "radius=" + str(filtersize))
IJ.run(imp_Threshold_1, "Subtract Background...", "rolling=50")
IJ.setAutoThreshold(imp_Threshold_1, threshold_method + " dark")
#Prefs.blackBackground = True;
IJ.run(imp_Threshold_1, "Convert to Mask", "")
return imp_Threshold_1
def get_threshold(imp, method):
# from ij.process import AutoThresholder
# from ij.process import ImageStatistics
# thresholder = AutoThresholder()
# stats = imp.getProcessor().getStatistics()
# value = thresholder.getThreshold(method, stats.histogram)
arg = "%s dark" % method
IJ.setAutoThreshold(imp, arg)
value = imp.getProcessor().getMinThreshold()
IJ.resetThreshold(imp)
return value
def process(imp):
try:
IJ.run(imp, "Subtract Background...", "rolling=50");
IJ.run(imp, "Subtract Background...", "rolling=50");
ImageConverter.setDoScaling(True);
IJ.run(imp, "32-bit", "");
IJ.run(imp, "Smooth", "");
IJ.setAutoThreshold(imp, "Default dark");
IJ.run(imp, "NaN Background", "");
return imp;
except(AttributeError):
print("error processing!");
def measureChannels(ROIset, imp, frameNumber):
rm = RoiManager.getInstance()
if not rm:
rm = RoiManager()
nChannels = imp.getNChannels()
for channel in range(nChannels):
target_imp = extractChannel(imp, channel + 1, frameNumber)
target_imp.show()
for roi in ROIset:
rm.setSelectedIndexes([roi])
IJ.setAutoThreshold(target_imp, "Huang dark")
rm.runCommand(target_imp, "Measure")
target_imp.close()
def getRadius(image):
IJ.run('8-bit')
Img = IJ.getImage()
IJ.run('Invert')
IJ.setAutoThreshold(Img, 'Default')
IJ.run('Convert to Mask')
# Must change units to pixels --> 10px. minimum
IJ.run(Img, 'Analyze Particles...', 'size=10-Infinity show=[Overlay Outlines] display clear')
rt = IJ.getTextPanel()
data = []
for line in range(rt.getLineCount()):
data.append(rt.getLine(line))
return data
def generateNucleusMask(nucIp, method="Otsu", stack=True, minNucleusSize=50):
nucMaskIp = nucIp.duplicate()
if not stack:
IJ.setAutoThreshold(nucMaskIp, "{} dark".format(method))
IJ.run(nucMaskIp, "Convert to Mask", "method={} background=Dark calculate".format(method))
else:
IJ.setAutoThreshold(nucMaskIp, "{} dark stack".format(method))
IJ.run(nucMaskIp, "Convert to Mask", "method={} background=Dark stack".format(method))
IJ.run(nucMaskIp, "Open", "stack")
IJ.run("Set Measurements...", "stack redirect=None decimal=3")
IJ.run(nucMaskIp, "Analyze Particles...", "size={}-Infinity circularity=0.2-1.00 show=Masks exclude in_situ stack".format(minNucleusSize))
IJ.run(nucMaskIp,"Fill Holes", "stack")
nucMaskIp.show()
return nucMaskIp
def apply_threshold(imp, method='Otsu',
background_threshold='dark',
stackopt=False,
corrf=1.0):
# one threshold value for the whole stack with correction
if stackopt:
# create argument string for the IJ.setAutoThreshold
thcmd = method + ' ' + background_threshold + ' stack'
# set threshold and get the lower threshold value
IJ.setAutoThreshold(imp, thcmd)
ip = imp.getProcessor()
# get the threshold value and correct it
lowth = ip.getMinThreshold()
lowth_corr = int(round(lowth * corrf, 0))
# process stack with corrected threshold value
imp = ThresholdTools.apply_threshold_stack_corr(imp, lowth_corr,
method=method)
# threshold slice-by-slice with correction
if not stackopt:
# get the stack
stack = imp.getStack() # get the stack within the ImagePlus
nslices = stack.getSize() # get the number of slices
print('Slices: ' + str(nslices))
print('Thresholding slice-by-slice')
for index in range(1, nslices + 1):
ip = stack.getProcessor(index)
# get the histogramm
hist = ip.getHistogram()
# get the threshold value
lowth = ThresholdTools.apply_autothreshold(hist, method=method)
lowth_corr = int(round(lowth * corrf, 0))
ip.threshold(lowth_corr)
# convert to 8bit without rescaling
ImageConverter.setDoScaling(False)
ImageConverter(imp).convertToGray8()
return imp
def getMask(imp, chan): dup = Duplicator() mask = dup.run(imp, chan, chan, 1,1, 1,1) sigma = 0.2 IJ.run(mask, "Gaussian Blur...", "sigma="+str(sigma)+" scaled") if chan==1: method = "Otsu" else: method = "MaxEntropy" IJ.setAutoThreshold(mask, method+" dark") Prefs.blackBackground = True IJ.run(mask, "Convert to Mask", "") IJ.run(mask, "Close-", "") IJ.run(mask, "Watershed", "") return mask
def Generate_segmented_bgsub(imp, channel, threshold_method, filtersize):
imp_Threshold_1 = ExtractChannel(imp1, channel)
imp_Threshold_1.setTitle(("Threshold" + "Channel" + str(channel)))
imp_Threshold_1.show()
IJ.run(imp_Threshold_1, "Select All", "")
stats = imp_Threshold_1.getStatistics(Measurements.MEAN
| Measurements.STD_DEV)
IJ.run(imp_Threshold_1, "Select None", "")
background = stats.mean + (2 * stats.stdDev)
IJ.run(imp_Threshold_1, "Subtract...", "value=" + str(background))
IJ.run(imp_Threshold_1, "Median...", "radius=" + str(filtersize))
IJ.run(imp_Threshold_1, "Subtract Background...", "rolling=50")
IJ.setAutoThreshold(imp_Threshold_1, threshold_method + " dark")
#Prefs.blackBackground = True;
IJ.run(imp_Threshold_1, "Convert to Mask", "")
return imp_Threshold_1
def countobjects(imp,
rt,
subtractBackground=False,
watershed=False,
dilate=False,
threshMethod="Otsu",
physicalUnits=True,
minSize=0.00,
maxSize=float("inf"),
minCirc=0.00,
maxCirc=1.00):
"""Threshold and count objects in channel 'channelNumber'.
This function splits an image in the separate channels, and counts the number of objects in the thresholded
channel.
Args:
imp: An ImagePlus with 1 frame, 1 slice.
Returns:
A list of filepaths.
"""
cal = imp.getCalibration()
if subtractBackground:
IJ.run(imp, "Subtract Background...", "rolling=50")
IJ.setAutoThreshold(imp, "{} dark".format(threshMethod))
IJ.run(imp, "Convert to Mask", "")
if dilate:
IJ.run(imp, "Dilate", "")
if watershed:
IJ.run(imp, "Watershed", "")
if physicalUnits: # Convert physical units to pixels for the current calibration.
minSize = cal.getRawX(math.sqrt(minSize))**2
maxSize = cal.getRawX(math.sqrt(maxSize))**2
pa = ParticleAnalyzer(
ParticleAnalyzer.SHOW_OVERLAY_OUTLINES
| ParticleAnalyzer.DISPLAY_SUMMARY, #int options
Measurements.AREA | Measurements.SHAPE_DESCRIPTORS | Measurements.MEAN
| Measurements.CENTROID | Measurements.LABELS, #int measurements
rt, #ResultsTable
minSize, #double
maxSize, #double
minCirc, #double
maxCirc) #double
pa.analyze(imp)
return imp
def SegmentMask(ip):
'''
Returns a Region of Interest (ROI) that contains a proposed segmentation for the input image processor imp
Binarization: Find the GaussianBlur with minimum radius necessary to perform a Minimum Autothreshold
'''
minThresholdValue=-1
radius=GaussianBlurParam['initialRadius'] #Initial Radius os the Gaussian Blur
contador=0
while (minThresholdValue==-1 and contador<6):
contador=contador+1
#Make a copy of the image
impThres = ImagePlus()
ipThres = ip.duplicate()
impThres.setProcessor("Copy for thresholding", ipThres)
GaussianBlur().blurGaussian( impThres.getProcessor(), radius, radius,GaussianBlurParam['accuracy'])
#impThres.show()
try:
IJ.setAutoThreshold(impThres, "Minimum dark")
minThresholdValue = impThres.getProcessor().getMinThreshold()
except:
print("No threshold found for segmentation")
if minThresholdValue !=-1:
#Check thresholded image contains at least 50% of the original
stats = impThres.getStatistics()
histogram = stats.histogram
binSize=(stats.max-stats.min)/256
ThresholdBin=int(round((minThresholdValue-stats.min)/binSize))
CumulativeValues=0
for i in range(ThresholdBin):
CumulativeValues+=histogram[i]
ImageAboveThreshold=1-float(CumulativeValues)/(ip.width*ip.height)
#(ImageAboveThreshold)
#ImageAboveThreshold must be above 50%
if ImageAboveThreshold < 0.5:
minThresholdValue=-1
radius=radius+1
impThres.getProcessor().setThreshold(minThresholdValue, stats.max, ImageProcessor.NO_LUT_UPDATE)
boundRoi = ThresholdToSelection.run(impThres)
return boundRoi
def renyiBinarization(self):
try:
IJ.selectWindow(self.primaryImage)
primaryImageID = IJ.getImage()
IJ.setAutoThreshold(primaryImageID, "RenyiEntropy dark")
IJ.setThreshold(self.primaryLowerThreshold,
self.primaryUpperThreshold)
IJ.run("Convert to Mask")
IJ.selectWindow(self.secondaryImage)
secondaryImageID = IJ.getImage()
IJ.setAutoThreshold(secondaryImageID, "RenyiEntropy dark")
IJ.setThreshold(self.secondaryLowerThreshold,
self.secondaryUpperThreshold)
IJ.run("Convert to Mask")
except:
print("unable to binarize images.")
finally:
return self
def analyze(image, outdir, index, size=10000):
"""Opens a file and creates masks."""
masks = []
imagetitle = image.getTitle().split(".")[0]
# segmentation
IJ.setAutoThreshold(image, "Default dark");
IJ.run(image, "Options...", "iterations=1 count=1 do=Nothing");
#IJ.run(mask, "Convert to Mask", "");
IJ.run(image, "Analyze Particles...", "size=0-"+str(size)+" show=Masks summarize display");
masks.append(IJ.getImage())
IJ.run(image, "Analyze Particles...", "size="+str(size)+"-infinity show=Masks summarize display");
masks.append(IJ.getImage())
# create multi-color merged mask
mergedmask = RGBStackMerge.mergeChannels(masks, False)
for m in masks:
m.close()
mergedmask.setTitle(imagetitle + "-"+str(index)+"-mask.tif")
outputfile = path.join(outdir, mergedmask.getTitle())
IJ.saveAs(mergedmask, "TIFF", outputfile)
def auto_threshold(imp, ch_name, is_auto_thresh, method="IsoData"):
if is_auto_thresh:
IJ.setAutoThreshold(imp, "{} dark".format(method))
thres_min = imp.getProcessor().getMinThreshold()
else:
imp.show()
IJ.run("Threshold...")
# this is the method to wait the user set up the threshold
wu = WaitForUserDialog("Set manual threshold for {}".format(ch_name), "Use slider to adjust threshold and press OK")
wu.show()
thres_min = imp.getProcessor().getMinThreshold()
thres_max = imp.getProcessor().getMaxThreshold()
IJ.log(" -- {}: Min threshold {}".format(ch_name, thres_min))
IJ.setThreshold(imp, thres_min, thres_max)
imp.hide()
WindowManager.getWindow("Threshold").close()
return thres_min
def create_mock_resultstable():
"""Creates small ResultsTable with fictive values"""
# Create a ImageJ ResultsTable, convert it into Omero table object, upload and link it to target object
imp = IJ.openImage("http://imagej.nih.gov/ij/images/blobs.gif")
imp.show()
mask = imp.duplicate()
IJ.run(mask, "Median...", "radius=2")
IJ.run(mask, "Options...", "iterations=1 count=1 black")
IJ.setAutoThreshold(mask, "Default")
IJ.run(mask, "Convert to Mask", "")
IJ.run(mask, "Watershed", "")
IJ.run(
mask, "Set Measurements...",
"area mean min centroid integrated display redirect=%s decimal=3" %
imp.getTitle())
IJ.run(mask, "Analyze Particles...",
"size=0-Infinity display exclude clear summarize add")
imp.close()
rt = ResultsTable.getResultsTable()
rt.show("Results")
return rt
def Segment_Nuclei(imp, channel):
imp_Threshold_1 = ExtractChannel(imp1, channel)
imp_Threshold_1.setTitle(("Threshold" + "Channel" + str(channel)))
imp_Threshold_1.show()
IJ.run(imp_Threshold_1, "Subtract...", "value=5000")
IJ.run(imp_Threshold_1, "Median...", "radius=3")
#IJ.run(imp_Threshold_1, "Subtract Background...", "rolling=500");
IJ.setAutoThreshold(imp_Threshold_1, "Li dark")
#Prefs.blackBackground = True;
IJ.run(imp_Threshold_1, "Convert to Mask", "")
IJ.run(imp_Threshold_1, "Erode", "")
IJ.run(imp_Threshold_1, "Erode", "")
IJ.run(imp_Threshold_1, "Erode", "")
IJ.run(imp_Threshold_1, "Erode", "")
IJ.run(imp_Threshold_1, "Erode", "")
IJ.run(imp_Threshold_1, "Dilate", "")
IJ.run(imp_Threshold_1, "Dilate", "")
IJ.run(imp_Threshold_1, "Dilate", "")
IJ.run(imp_Threshold_1, "Dilate", "")
IJ.run(imp_Threshold_1, "Dilate", "")
#IJ.run(imp_Threshold_1, "Dilate", "");
return imp_Threshold_1
def generateCardiomyocyteMask(cmIp, method="Otsu", stack=True, minCmSize=500, brightfield = False):
cmIp.setTitle("CmStain")
if brightfield:
IJ.run(cmIp, "Find Edges", "stack")
if not stack:
IJ.setAutoThreshold(cmIp, "{} dark".format(method))
IJ.run(cmIp, "Convert to Mask", "method={} background=Dark calculate".format(method))
else:
IJ.setAutoThreshold(cmIp, "{} dark stack".format(method))
IJ.run(cmIp, "Convert to Mask", "method={} background=Dark stack".format(method))
if brightfield:
IJ.run(cmIp, "Morphological Filters (3D)", "operation=Closing element=Ball x-radius=2 y-radius=2 z-radius=0")
delIp = cmIp
delIp.changes = False
delIp.close()
cmIp = WindowManager.getImage("CmStain-Closing")
IJ.run(cmIp,"Fill Holes", "stack")
cmIp.show()
IJ.run("Set Measurements...", "stack redirect=None decimal=3")
IJ.run(cmIp, "Analyze Particles...", "size={}-Infinity show=[Masks] exclude in_situ stack".format(cmMinSize))
cmMaskIp = cmIp.duplicate()
IJ.run(cmIp, "Analyze Particles...", "size={}-Infinity show=[Count Masks] exclude in_situ stack".format(cmMinSize))
cmMaskIp.show(), cmIp.show()
return cmIp, cmMaskIp
def prepareImage(passDir, passFile, passOutput, passPixels, passBlur, passThreshold):
# Attempt to open as image, exit if not
fullPath = os.path.join(passDir, passFile)
retImage = IJ.openImage(fullPath)
if not retImage: return None
retImage.show()
# Resize canvas to prepare for fast rotations, select original
imgWidth = retImage.getWidth()
imgHeight = retImage.getHeight()
maxDim = math.sqrt(imgWidth ** 2 + imgHeight ** 2)
borderX = (maxDim - imgWidth)/2
borderY = (maxDim - imgHeight)/2
IJ.run("Canvas Size...", "width={0} height={0} position=Center".format(maxDim))
IJ.makeRectangle(borderX, borderY, imgWidth, imgHeight)
# Set scale to pixels (will manually calculate later)
IJ.run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
# Blur "overhanging" projections
IJ.run("Gaussian Blur...", "sigma={0}".format(passBlur))
# Set threshold
IJ.setAutoThreshold(retImage, "{0} dark apply".format(passThreshold))
IJ.makeRectangle(0, 0, retImage.getWidth(), retImage.getHeight())
# Analyze particles and obtain outline image
IJ.run("Analyze Particles...", "size={0}-Infinity show=Outlines pixel clear".format(passPixels));
IJ.selectWindow("Drawing of {0}".format(retImage.getTitle()))
fileParts = passFile.split(".")
IJ.save(os.path.join(passOutput, "{0}-outline-{1}.{2}".format(fileParts[0], passThreshold, '.'.join(fileParts[1:]))))
IJ.run("Close")
return retImage
def analyze_homogeneity(image_title):
IJ.selectWindow(image_title)
raw_imp = IJ.getImage()
IJ.run(raw_imp, "Duplicate...", "title=Homogeneity duplicate")
IJ.selectWindow('Homogeneity')
hg_imp = IJ.getImage()
# Get a 2D image
if hg_imp.getNSlices() > 1:
IJ.run(hg_imp, "Z Project...", "projection=[Average Intensity]")
hg_imp.close()
IJ.selectWindow('MAX_Homogeneity')
hg_imp = IJ.getImage()
hg_imp.setTitle('Homogeneity')
# Blur and BG correct the image
IJ.run(hg_imp, 'Gaussian Blur...', 'sigma=' + str(HOMOGENEITY_RADIUS) + ' stack')
# Detect the spots
IJ.setAutoThreshold(hg_imp, HOMOGENEITY_THRESHOLD + " dark")
rm = RoiManager(True)
table = ResultsTable()
pa = ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER,
ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES,
Measurements.AREA, # measurements
table, # Output table
0, # MinSize
500, # MaxSize
0.0, # minCirc
1.0) # maxCirc
pa.setHideOutputImage(True)
pa.analyze(hg_imp)
areas = table.getColumn(table.getHeadings().index('Area'))
median_areas = compute_median(areas)
st_dev_areas = compute_std_dev(areas, median_areas)
thresholds_areas = (median_areas - (2 * st_dev_areas), median_areas + (2 * st_dev_areas))
roi_measurements = {'integrated_density': [],
'max': [],
'area': []}
IJ.setForegroundColor(0, 0, 0)
for roi in rm.getRoisAsArray():
hg_imp.setRoi(roi)
if REMOVE_CROSS and hg_imp.getStatistics().AREA > thresholds_areas[1]:
rm.runCommand('Fill')
else:
roi_measurements['integrated_density'].append(hg_imp.getStatistics().INTEGRATED_DENSITY)
roi_measurements['max'].append(hg_imp.getStatistics().MIN_MAX)
roi_measurements['integrated_densities'].append(hg_imp.getStatistics().AREA)
rm.runCommand('Delete')
measuremnts = {'mean_integrated_density': compute_mean(roi_measurements['integrated_density']),
'median_integrated_density': compute_median(roi_measurements['integrated_density']),
'std_dev_integrated_density': compute_std_dev(roi_measurements['integrated_density']),
'mean_max': compute_mean(roi_measurements['max']),
'median_max': compute_median(roi_measurements['max']),
'std_dev_max': compute_std_dev(roi_measurements['max']),
'mean_area': compute_mean(roi_measurements['max']),
'median_area': compute_median(roi_measurements['max']),
'std_dev_area': compute_std_dev(roi_measurements['max']),
}
# generate homogeinity image
# calculate interpoint distance in pixels
nr_point_columns = int(sqrt(len(measuremnts['mean_max'])))
# TODO: This is a rough estimation that does not take into account margins or rectangular FOVs
inter_point_dist = hg_imp.getWidth() / nr_point_columns
IJ.run(hg_imp, "Maximum...", "radius="+(inter_point_dist*1.22))
# Normalize to 100
IJ.run(hg_imp, "Divide...", "value=" + max(roi_measurements['max'] / 100))
IJ.run(hg_imp, "Gaussian Blur...", "sigma=" + (inter_point_dist/2))
hg_imp.getProcessor.setMinAndMax(0, 255)
# Create a LUT based on a predefined threshold
red = zeros(256, 'b')
green = zeros(256, 'b')
blue = zeros(256, 'b')
acceptance_threshold = HOMOGENEITY_ACCEPTANCE_THRESHOLD * 256 / 100
for i in range(256):
red[i] = (i - acceptance_threshold)
green[i] = (i)
homogeneity_LUT = LUT(red, green, blue)
hg_imp.setLut(homogeneity_LUT)
return hg_imp, measuremnts
imp = IJ.openImage(
"/Users/jrminter/Desktop/Pella_617_Au_on_C_100kX_15kV_cr.tif")
imp.setTitle("Orig")
imp.show()
imp_proc = imp.duplicate()
imp_proc.setTitle("Proc")
IJ.run(imp_proc, "Median...", "radius=2")
IJ.run(imp_proc, "Invert", "")
IJ.run(imp_proc, "Enhance Contrast", "saturated=0.35")
imp_proc.show()
imp_bin = imp_proc.duplicate()
imp_bin.setTitle("Bin")
IJ.setAutoThreshold(imp_bin, "MinError")
imp_bin.show()
IJ.run("Make Binary")
imp_seg = imp_bin.duplicate()
imp_seg.setTitle("Seg")
IJ.run("Set Measurements...",
"area mean perimeter fit shape display add redirect=Orig decimal=3")
IJ.run(
imp_seg, "Analyze Particles...",
"size=20-Infinity circularity=0.3-1.00 show=[Overlay Masks] display exclude clear add"
)
# rm.runCommand(imp_seg,"Show None")
rm.runCommand(imp, "Show All with labels")
imp_seg.show()
imp_ori.show()
def startTracking(filepath, fdir, ffile, filename):
outpath = fdir
troutpath = fdir + separator + ffile + separator + "tracked" + separator
stackoutpath = fdir + separator + ffile + separator + "stacks" + separator
pixwidth = 0.647
interval_sec = 600 #pr
if "141006" in fdir:
interval_sec = 600
elif "141117" in fdir:
interval_sec = 300
elif "141215" in fdir:
interval_sec = 300
if not os.path.isdir(outpath):
os.mkdir(outpath)
if not os.path.isdir(troutpath):
os.mkdir(troutpath)
if not os.path.isdir(stackoutpath):
os.mkdir(stackoutpath)
print 'filepath: ', filepath #pr
print 'fdir: ', fdir #pr
print 'ffile: ', ffile #pr
IJ.run("Image Sequence...",
"open=" + filepath + " file=" + filename + " sort")
#pr
#IJ.run("Image Sequence...", "open=" + filepath + " file=molm sort"); #pr
imp = WindowManager.getCurrentImage()
imptitle = imp.getTitle()
nframes = imp.getNSlices()
IJ.run(
imp, "Properties...", "channels=1 slices=1 frames=" + str(nframes) +
" unit=inch pixel_width=" + str(pixwidth) + " pixel_height=" +
str(pixwidth) + " voxel_depth=1.0000 frame=[" + str(interval_sec) +
" sec]")
IJ.run(imp, "Duplicate...", "title=" + imptitle + "_dup duplicate")
imp_dup = WindowManager.getImage(imptitle + "_dup")
IJ.run(imp_dup, "Gaussian Blur...", "sigma=50 stack")
ic = ImageCalculator()
imp_corr = ic.run("Divide create 32-bit stack", imp, imp_dup)
imp_corr.setTitle(imptitle + "_corrected")
imp_corr.show()
imp.changes = False
imp.close()
imp_dup.changes = False
imp_dup.close()
IJ.run(imp_corr, "8-bit", "")
IJ.run(
imp_corr, "Normalize Local Contrast",
"block_radius_x=100 block_radius_y=100 standard_deviations=1 stretch stack"
)
IJ.saveAs(imp_corr, "Tiff",
stackoutpath + separator + imptitle + "_corrected.tif")
IJ.run(imp_corr, "Duplicate...", "title=" + imptitle + "_bg duplicate")
imp_bg = WindowManager.getImage(imptitle + "_bg")
#Prefs.blackBackground = True;
IJ.setAutoThreshold(imp_bg, "MinError dark")
IJ.run(imp_bg, "Convert to Mask", "stack")
IJ.run(imp_bg, "Analyze Particles...",
"size=10000-Infinity show=Masks stack")
imp_bg.changes = False
imp_bg.close()
imp_bgmask = WindowManager.getImage("Mask of " + imptitle + "_bg")
ic = ImageCalculator()
imp_corr_wobg = ic.run("Subtract create stack", imp_corr, imp_bgmask)
imp_corr_wobg.setTitle(imptitle + "_corrected_womask")
imp_corr_wobg.show()
IJ.saveAs(imp_corr_wobg, "Tiff",
stackoutpath + separator + imptitle + "_corrected_womask.tif")
#pr
# pr: substract average frames
zp = ZProjector(imp_corr_wobg)
zp.setMethod(ZProjector.AVG_METHOD)
zp.doProjection()
zpimp = zp.getProjection()
zpimp.show()
imp_corr_wobg_sub = ImageCalculator().run("Subtract create stack",
imp_corr_wobg, zpimp)
imp_corr_wobg_sub.show()
#imp_corr_wobg.changes = False
#imp_corr_wobg.close()
# pr: subtract average frames (END)
IJ.saveAs(
imp_corr_wobg_sub, "Tiff", stackoutpath + separator + imptitle +
"_corrected_womask_substracted.tif")
#pr
IJ.saveAs(
zpimp, "Tiff",
stackoutpath + separator + imptitle + "_corrected_womask_avg.tif")
#commented out: pr
#IJ.saveAs(imp_corr_wobg, "Tiff", stackoutpath+separator+imptitle+"_corrected_womask.tif");
IJ.saveAs(imp_bgmask, "Tiff",
stackoutpath + separator + imptitle + "_bgmask.tif")
print(stackoutpath + separator + imptitle +
"_corrected_womask_substracted.tif")
print(stackoutpath + separator + imptitle + "_corrected_womask_avg.tif")
print(stackoutpath + separator + imptitle + "_bgmask.tif")
imp_corr.changes = False
imp_corr.close()
imp_bgmask.changes = False
imp_bgmask.close()
imp_corr_wobg.changes = False
imp_corr_wobg.close()
#imp_corr_wobg_sub.changes = False
#imp_corr_wobg_sub.close()
zpimp.changes = False
zpimp.close()
#IJ.log(System.getProperty("os.name"))
#IJ.log(fdir)
return imp_corr_wobg_sub
def updatepressed(event):
self.__image=IJ.getImage()
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
rm.runCommand("reset")
self.__image.killRoi()
IJ.run("Threshold...")
IJ.setAutoThreshold(self.__image, "MaxEntropy")
rt=ResultsTable()
pa=ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER+ParticleAnalyzer.CLEAR_WORKSHEET , Measurements.AREA+Measurements.ELLIPSE+Measurements.MEAN, rt, 0.00, 10000.00, 0.00, 1.00)
pa.analyze(self.__image)
self.__roisArray=[]
self.__roisArray=rm.getRoisAsArray()
#for i in range(rm.getCount()) :
# rm.select(i)
# rm.runCommand("Set Color", "0000FF", 2)
IJ.resetThreshold(self.__image)
rt.show("tempRT")
areas=rt.getColumn(ResultsTable.AREA)
means=rt.getColumn(ResultsTable.MEAN)
majors=rt.getColumn(ResultsTable.MAJOR)
minors=rt.getColumn(ResultsTable.MINOR)
#print 0
if self.__slidersDict["Area_max"].getMaximum() < int(max(areas)+1):
# print 1
self.__slidersDict["Area_max"].setMaximum(int(max(areas))+1)
if self.__slidersDict["Area_min"].getMaximum() < int(max(areas)+1):
# print 2
self.__slidersDict["Area_min"].setMaximum(int(max(areas))+1)
if self.__slidersDict["Mean_max"].getMaximum() < int(max(means)+1):
# print 3
self.__slidersDict["Mean_max"].setMaximum(int(max(means))+1)
if self.__slidersDict["Mean_min"].getMaximum() < int(max(means)+1):
# print 4
self.__slidersDict["Mean_min"].setMaximum(int(max(means))+1)
if self.__slidersDict["Major_max"].getMaximum() < int(max(majors)):
# print 5
self.__slidersDict["Major_max"].setMaximum(int(max(majors))+1)
if self.__slidersDict["Major_min"].getMaximum() < int(max(majors)+1):
# print 6
self.__slidersDict["Major_min"].setMaximum(int(max(majors))+1)
if self.__slidersDict["Minor_max"].getMaximum() < int(max(minors)+1):
# print 7
self.__slidersDict["Minor_max"].setMaximum(int(max(minors))+1)
if self.__slidersDict["Minor_min"].getMaximum() < int(max(minors)+1):
# print 8
self.__slidersDict["Minor_min"].setMaximum(int(max(minors))+1)
if self.__slidersDict["AR_max"].getMaximum() < int((max(majors)+1)/min(minors)+1):
# print 9
self.__slidersDict["AR_max"].setMaximum(int((max(majors)+1)/(min(minors))))
if self.__slidersDict["AR_min"].getMaximum() < int((max(majors)+1)/min(minors)):
# print 10
self.__slidersDict["AR_min"].setMaximum(int((max(majors)+1)/(min(minors))))
#print 11
for sb in self.__slidersDict.values():
sb.repaint()
#rm.runCommand("reset")
#temprois=self.getIncludeRois()
#IJ.run(self.__image, "Remove Overlay", "")
#o=Overlay()
#for roi in temprois:
# o.addElement(roi)
#self.__image.killRoi()
#self.__image.setOverlay(o)
self.__image.updateAndDraw()
# 2014-11-27 JRM 1.1.00 Get result from summary table
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
from ij import IJ, WindowManager
from ij.measure import ResultsTable
from ij.text import TextWindow
bClose = True
IJ.run("Blobs (25K)")
imp = IJ.getImage()
IJ.setAutoThreshold(imp, "Default")
IJ.run(imp, "Convert to Mask", "")
IJ.run(imp, "Set Measurements...", "area center redirect=None decimal=3")
IJ.run(imp, "Analyze Particles...", "display exclude clear include summarize")
tw = WindowManager.getFrame("Summary")
if tw != None:
st = tw.getTextPanel().getResultsTable()
IJ.log("1st row of Summary:\n"+ st.getRowAsString(0))
v = st.getCounter()
w = st.getLastColumn()
s = st.size()
z = st.getValueAsDouble(w, 0)
af = float(z)
af /= 100.
print("Area Fraction: %.3f" % af)
IJ.run("Close All", "")
# access to the folder and the files in it
directory = File(folder)
listOfFilesInFolder = directory.listFiles()
for file in listOfFilesInFolder:
if (file.toString().endswith(".tif")):
# load image and show it
imp = IJ.openImage(file.toString())
imp.show()
copy = Duplicator().run(imp)
# apply a threshold to detect objects (cells, nuclei,...)
IJ.setAutoThreshold(imp, "Otsu")
Prefs.blackBackground = False
IJ.run(imp, "Convert to Mask", "")
# analyse objects and put results in table
IJ.run("Set Measurements...", "area display redirect=None decimal=5")
IJ.run(imp, "Analyze Particles...", "exclude add")
manager = RoiManager.getRoiManager()
manager.runCommand("Save",
file.toString() + ".RoiSet.zip")
for roi in manager.getRoisAsArray():
copy.setRoi(roi)
copy.show()
IJ.run(copy, "Enlarge...", "enlarge=-2")
def main(imp):
# We may want to set specific options depending on whether we are parsing a
# 2D or a 3D image. If the image has multiple channels/time points, we set
# the C,T position to be analyzed by activating them. The channel and frame
# will be stored in the profile properties map and can be retrieved later):
if imp.getNSlices() == 1:
parser = ImageParser2D(imp, context)
parser.setRadiiSpan(0, ImageParser2D.MEAN) # mean of 4 measurements at every radius
parser.setPosition(1, 1, 1) # channel, frame, Z-slice
else:
parser = ImageParser3D(imp, context)
parser.setSkipSingleVoxels(True) # ignore isolated voxels
parser.setPosition(1, 1) # channel, frame
# Segmentation: we can set the threshold manually using one of 2 ways:
# 1. manually: parser.setThreshold(lower_t, upper_t)
# 2. from the image itself: e.g., IJ.setAutoThreshold(imp, "Huang")
# If the image is already binarized, we can skip setting threshold levels:
if not (imp.isThreshold() or imp.getProcessor().isBinary()):
from ij import IJ
IJ.setAutoThreshold(imp, "Otsu dark")
# Center: the x,y,z coordinates of center of analysis. In a real-case usage
# these would be retrieved from ROIs or a centroid of a segmentation routine.
# If no ROI exists coordinates can be set in spatially calibrated units
# (floats) or pixel coordinates (integers):
if imp.getRoi() is None:
xc = int(round(imp.getWidth()/2))
yc = int(round(imp.getHeight()/2))
zc = int(round(imp.getNSlices()/2))
parser.setCenterPx(xc, yc, zc) # center of image
else:
parser.setCenterFromROI()
# Sampling distances: start radius (sr), end radius (er), and step size (ss).
# A step size of zero would mean 'continuos sampling'. Note that end radius
# could also be set programmatically, e.g., from a ROI
parser.setRadii(10, 5, parser.maxPossibleRadius()) # (sr, er, ss)
# We could now set further options as we would do in the dialog prompt:
parser.setHemiShells('none')
# (...)
# Parse the image. This may take a while depending on image size. 3D images
# will be parsed using the number of threads specified in ImageJ's settings:
parser.parse()
if not parser.successful():
log.error(imp.getTitle() + " could not be parsed!!!")
return
# We can e.g., access the 'Sholl mask', a synthetic image in which foreground
# pixels have been assigned the no. of intersections:
parser.getMask().show()
# Now we can access the Sholl profile:
profile = parser.getProfile()
if profile.isEmpty():
log.error("All intersection counts were zero! Invalid threshold range!?")
return
# We can now access all the measured data stored in 'profile': Let's display
# the sampling shells and the detected sites of intersections (NB: If the
# image already has an overlay, it will be cleared):
profile.getROIs(imp)
# For now, lets's perform a minor cleanup of the data and plot it without
# doing any polynomial regression. Have a look at Sholl_Extensive_Stats_Demo
# script for details on how to analyze profiles with detailed granularity
profile.trimZeroCounts()
profile.plot().show()
input_image_plus = IJ.openImage( input )
# Create a copy of the image.
input_image_plus_copy = input_image_plus.duplicate()
image_processor_copy = input_image_plus_copy.getProcessor()
try:
# Convert image to binary if necessary.
if not image_processor_copy.isBinary():
# Convert the image to binary grayscale.
IJ.run( input_image_plus_copy, "Make Binary","iterations=1 count=1 edm=Overwrite do=Nothing" )
# Set the options.
if jython_utils.asbool( dark_background ):
method_str = "%s dark" % method
else:
method_str = method
IJ.setAutoThreshold( input_image_plus_copy, method_str )
if display == "red":
display_mode = "Red"
elif display == "bw":
display_mode = "Black & White"
elif display == "over_under":
display_mode = "Over/Under"
IJ.setThreshold( input_image_plus_copy, threshold_min, threshold_max, display_mode )
# Run the command.
IJ.run( input_image_plus_copy, "threshold", "" )
# Save the ImagePlus object as a new image.
IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
except Exception, e:
jython_utils.handle_error( error_log, str( e ) )
