def findclearcell(inDir, currentDir, fileName):
print "Opening", fileName
file_path= os.path.join(currentDir, fileName)
options = ImporterOptions()
options.setId(file_path)
options.setSplitChannels(True)
imps = BF.openImagePlus(options)
for imp in imps:
imp.show()
if not imps:
return
IJ.selectWindow(fileName + " - C=2")
IJ.run("Close")
IJ.selectWindow(fileName + " - C=1")
IJ.run("Close")
IJ.selectWindow(fileName + " - C=0")
IJ.run("Close")
IJ.selectWindow(fileName + " - C=3")
IJ.run("8-bit")
IJ.run("Options...", "iterations=1 count=1 black edm=8-bit")
IJ.setThreshold(62, 255)
IJ.run("Convert to Mask", "method=Default backgorund=Dark black")
Macro.setOptions("Stack position")
for n in range(4,15):
n+=1
IJ.setSlice(n)
IJ.run(imp, "Analyze Particles...", "size=7.2-9 circularity=0.7-0.95 display")
def analyzeImage(passImage, passModel, passChannel, passProbability,
passPixels, passOutput):
retResults = list()
windows = set()
# Register current window
registerWindow(passImage.title, windows)
# Extract the requested channel
IJ.run("Z Project...", "projection=[Max Intensity]")
registerWindow("MAX_" + passImage.title, windows)
IJ.run("Duplicate...", "title=temp")
registerWindow("temp", windows)
# Apply WEKA training model to image
wekaSeg = WekaSegmentation(WindowManager.getCurrentImage())
wekaSeg.loadClassifier(passModel)
wekaSeg.applyClassifier(True)
# Extract first slice of probability map
wekaImg = wekaSeg.getClassifiedImage()
wekaImg.show()
registerWindow("Probability maps", windows)
IJ.setSlice(1)
IJ.run("Duplicate...", "title=temp2")
registerWindow("temp2", windows)
# Apply threshold and save
IJ.setThreshold(passProbability, 1, "Black & White")
fileParts = passImage.getTitle().split(".")
IJ.save(
os.path.join(
passOutput, "{0}-probmap.png".format(fileParts[0],
'.'.join(fileParts[1:]))))
# Perform particle analysis and save
IJ.run("Analyze Particles...",
"size={0}-Infinity show=Outlines pixel clear".format(passPixels))
registerWindow("Drawing of temp2", windows)
IJ.save(
os.path.join(
passOutput, "{0}-particles.png".format(fileParts[0],
'.'.join(fileParts[1:]))))
# Get measurements
tableResults = ResultsTable.getResultsTable()
for rowIdx in range(tableResults.size()):
retResults.append(tableResults.getRowAsString(rowIdx).split())
retResults[-1].insert(
0,
WindowManager.getCurrentImage().getCalibration().unit)
retResults[-1].append(
float(retResults[-1][4]) / float(retResults[-1][3]))
# Close windows
closeWindows(windows)
return retResults
def analyzeImage(passImage, passModel, passProbability, passPixels,
passOutput):
retResults = list()
# Apply WEKA training model to image
wekaSeg = WekaSegmentation(passImage)
wekaSeg.loadClassifier(passModel)
wekaSeg.applyClassifier(True)
# Extract first slice of probability map
wekaImg = wekaSeg.getClassifiedImage()
wekaImg.show()
IJ.selectWindow("Probability maps")
IJ.setSlice(1)
IJ.run("Duplicate...", "title=temp")
# Apply threshold and save
IJ.setThreshold(passProbability, 1, "Black & White")
fileParts = passImage.getTitle().split(".")
IJ.save(
os.path.join(
passOutput, "{0}-probmap.png".format(fileParts[0],
'.'.join(fileParts[1:]))))
# Perform particle analysis and save
IJ.run("Analyze Particles...",
"size={0}-Infinity show=Outlines pixel clear".format(passPixels))
IJ.selectWindow("Drawing of temp")
IJ.save(
os.path.join(
passOutput, "{0}-particles.png".format(fileParts[0],
'.'.join(fileParts[1:]))))
# Get measurements (skip final row, this will correspond to legend)
tableResults = ResultsTable.getResultsTable()
for rowIdx in range(tableResults.size() - 1):
retResults.append(tableResults.getRowAsString(rowIdx).split())
# Close interim windows
IJ.run("Close")
IJ.selectWindow("temp")
IJ.run("Close")
IJ.selectWindow("Probability maps")
IJ.run("Close")
return retResults
def mkMask(imp,prePick,numRep,nStacks):
file_name = imp.getTitle()
IJ.selectWindow(file_name)
IJ.setSlice(prePick)
tempFileNames=[]
for pp in range(0,numRep):
tempFileNames.append('temp'+str(pp))
IJ.run(imp,"Duplicate...", "title=" +tempFileNames[pp])
IJ.run("8-bit", "")
cont_imgs = " ".join('image%d=%s' %(c+1,w) for c,w in enumerate(tempFileNames))
IJ.run("Concatenate...", "title=tempStack " +cont_imgs)
tempStack = IJ.getImage()
IJ.run(tempStack,"Make Montage...", "columns="+str(numRep/nStacks)+" rows="+str(nStacks)+" scale=1 first=1 last="+str(numRep)+" increment=1 border=1 font=12")
m2_imp=IJ.getImage()
m2_imp.setTitle("Mask")
tempStack.close()
return m2_imp
def mkMask(imp,prePick,numRep,nStacks):
file_name = imp.getTitle()
IJ.selectWindow(file_name)
IJ.setSlice(prePick)
tempFileNames=[]
for pp in range(0,numRep):
tempFileNames.append('temp'+str(pp))
IJ.run(imp,"Duplicate...", "title=" +tempFileNames[pp])
IJ.run("8-bit", "")
cont_imgs = " ".join('image%d=%s' %(c+1,w) for c,w in enumerate(tempFileNames))
IJ.run("Concatenate...", "title=tempStack " +cont_imgs)
tempStack = IJ.getImage()
IJ.run(tempStack,"Make Montage...", "columns="+str(numRep/nStacks)+" rows="+str(nStacks)+" scale=1 first=1 last="+str(numRep)+" increment=1 border=1 font=12")
m2_imp=IJ.getImage()
m2_imp.setTitle("Mask")
tempStack.close()
return m2_imp
anno_width, anno_height, t_a + t_b + t_c)
# Add leading texts
labelTextAll(start=0, interval=1, x=10, y=40, fontsize=36,
text='[Flow:L--->R]')
# Add timestamps for each segment
x_ts, y_ts, fs_ts = 325, 30, 36 # x, y, and font_size
labelTimestamps(start=0, interval=sample_rate,
x=x_ts, y=y_ts, fontsize=fs_ts,
range0=1, range1=t_a)
labelTimestamps(start=int(t0_b - t0_a), interval=sample_rate,
x=x_ts, y=y_ts, fontsize=fs_ts,
range0=(t_a + 1), range1=(t_a + t_b))
labelTimestamps(start=int(t0_c - t0_a), interval=sample_rate,
x=x_ts, y=y_ts, fontsize=fs_ts,
range0=(t_a + t_b + 1), range1=(t_a + t_b + t_c))
# Add scale bar
labelTextAll(start=0, interval=1, x=700, y=20, fontsize=36,
text=(str(sbar_um) + um))
IJ.setBackgroundColor(255, 255, 255)
for i in range(1, t_a + t_b + t_c + 1):
IJ.setSlice(i)
IJ.makeRectangle(anno_width - 120 - sbar_px, 14, sbar_px, 16)
IJ.run('Cut')
# Save annotation banner
path = SaveDialog(title, title, '.tif').getDirectory()
IJ.run('Save', 'save=[' + path + title + ']')
def analyzeImage(passImage, passModel, passProbability, passOutput):
retResults = list()
# Apply weka training model to image
wekaSeg = WekaSegmentation(passImage)
wekaSeg.loadClassifier(passModel)
wekaSeg.applyClassifier(True)
# Extract probability map
wekaImg = wekaSeg.getClassifiedImage()
wekaImg.show()
IJ.run("Clear Results")
# Process each slice
for sliceIdx in range(ROW_BACKGROUND + 1):
# Select slice and duplicate
IJ.selectWindow("Probability maps")
IJ.setSlice(sliceIdx + 1)
IJ.run("Duplicate...", "title=temp")
# Apply threshold to probability
IJ.setThreshold(passProbability, 1, "Black & White")
# For background, take inverse
if sliceIdx == ROW_BACKGROUND: IJ.run("Invert")
# Change background to NaN for area, then measure
IJ.run("NaN Background", ".")
IJ.run("Measure")
# Save image to output directory
fileParts = passImage.getTitle().split(".")
IJ.save(
os.path.join(
passOutput,
"{0}-{1}.{2}".format(fileParts[0], FILE_TYPE[sliceIdx],
'.'.join(fileParts[1:]))))
IJ.selectWindow("temp")
IJ.run("Close")
# Close probability maps
IJ.selectWindow("Probability maps")
IJ.run("Close")
# Obtain results
tempResults = list()
tableResults = ResultsTable.getResultsTable()
for rowIdx in range(tableResults.size()):
tempResults.append(
[float(x) for x in tableResults.getRowAsString(rowIdx).split()])
# Compile image statistics as M/(M+F), F/(M+F), M/total, F/total, U/total, E/total, M+F, total
mfTotal = tempResults[ROW_MALE][FIELD_AREA] + tempResults[ROW_FEMALE][
FIELD_AREA]
total = tempResults[ROW_BACKGROUND][FIELD_AREA]
retResults.append(tempResults[ROW_MALE][FIELD_AREA] / mfTotal)
retResults.append(tempResults[ROW_FEMALE][FIELD_AREA] / mfTotal)
retResults.append(tempResults[ROW_MALE][FIELD_AREA] / total)
retResults.append(tempResults[ROW_FEMALE][FIELD_AREA] / total)
retResults.append(tempResults[ROW_UNDIF][FIELD_AREA] / total)
retResults.append(tempResults[ROW_EXTRA][FIELD_AREA] / total)
retResults.append(mfTotal)
retResults.append(total)
return retResults
def setSlice(index):
IJ.setSlice(index)
IJ.run("Set Measurements...",
"area integrated display redirect=None decimal=3")
IJ.run("Clear Results")
IJ.run("Split Channels")
myelin = "C" + str(myelinCH) + "-" + title
points = "C" + str(pointsCH) + "-" + title
rt = ResultsTable.getResultsTable(
) #This object allows us to change the labels in the results table
#Threshold the myelin stack
IJ.selectWindow(myelin)
IJ.run("8-bit")
if interactive == 1:
for plane in range(1, n_slices + 1):
IJ.setSlice(plane)
message = wait(
"Threshold",
"Click OK when you have finished selecting a threshold for plane %s"
% plane)
message.show()
IJ.run("Convert to Mask", "method=Default background=Dark only")
IJ.run("Invert", "stack")
else:
IJ.run("Convert to Mask", "method=Default background=Dark calculate")
IJ.run("Median...", "radius=%s stack" % median)
IJ.run("Fill Holes", "stack")
IJ.run("Close-", "stack")
for i in range(iterations):
IJ.run("Dilate", "stack")
#print r1.getFloatPolygon().xpoints[0] #get xpoint
#first convert our ROIs to something more useful, a tuple containing the point (x,y) and the Z position => (x,y,z)
for i in range(0, nRois-1):
roi1 = rm.getRoi(i)
roi2 = rm.getRoi(i+1)
pt1 = (roi1.getFloatPolygon().xpoints[0],roi1.getFloatPolygon().ypoints[0],roi1.getPosition())
pt2 = (roi2.getFloatPolygon().xpoints[0],roi2.getFloatPolygon().ypoints[0],roi2.getPosition())
startSlice = pt1[2]
endSlice = pt2[2]
nSlices = (endSlice - startSlice)
xcorrect = (pt1[0]-pt2[0]);
ycorrect = (pt1[1]-pt2[1]);
print "Point pair: "
print pt1
print pt2
IJ.setSlice(pt1[2]) #set starting slice
driftx = xcorrect/nSlices;
offsetx = 0;
print "startSlice: %s ;endSlice: %s" % (startSlice, endSlice)
print "nSlices: %s" % (nSlices,)
for j in range(startSlice, totSlices+1):
IJ.setSlice(j)
if j <= endSlice:
offsetx += driftx
IJ.run("Translate...", "interpolation=Bicubic slice y=0 x="+str(offsetx));
drifty = ycorrect/nSlices;
offsety = 0;
for k in range(startSlice, totSlices+1):
IJ.setSlice(k)
if k <= endSlice:
def to_golgi_channel():
if golgi_c != "-":
IJ.setSlice(int(golgi_c))
else:
pass
def to_transport_channel():
if transport_c != "-":
IJ.setSlice(int(transport_c))
else:
pass
imp = IJ.getImage()
image_name = imp.title
bit_depth = bit_tester(image_name)
colorscale()
#set a manual background value#
if man_bck_det is True:
if current_image != image_name:
IJ.setTool("oval")
region = "Select Background"
selection(region)
to_transport_channel()
man_bck_list=[]
for channel in channel_iterator:
channel_first = int(channel)
IJ.setSlice(channel_first)
man_bck_list.append(selection_mean())
background = man_bck_list[0]
to_transport_channel()
if mean_max_det is True:
IJ.setTool("polygon")
else:
IJ.setTool("rectangle")
count_options = 0
if count_options == 1: # asks if we are looking at a new image
getOptions(dest)
region = "select cell"
selection(region)
IJ.run("Duplicate...", "duplicate")
num_tracks = track_model.nTracks(true)
trackID = track_model.trackIDs(true).toArray()
track_position_list = []
if num_tracks > 1:
warning_blurb = 'WARNING: Multiple tracks passing thresholds were found in image C1_'
warning_fileID.write(warning_blurb + image_stack + "\n")
if num_tracks == 0:
warning_blurb = 'WARNING: No tracks passing thresholds were found in image C1_'
warning_fileID.write(warning_blurb + image_stack + "\n")
IJ.selectWindow(file_name)
IJ.run('Z Project...', 'projection=[Max Intensity] all')
IJ.run('Duplicate...', 'duplicate frames=1')
IJ.setSlice(1)
IJ.run('Enhance Contrast', 'saturated=0.05')
IJ.setSlice(2)
IJ.run('Enhance Contrast', 'saturated=0.05')
IJ.run('RGB Color')
imp_max = IJ.getImage()
save_filename = image_directory + 'Track_Labels/' + file_name + '/Max_' + file_name
IJ.save(save_filename)
if len(trackID) > 0:
for i in trackID:
## Initialize variables
track_max_frame = 0
min_frame = max_frames
vis_track = i
track_spots = track_model.trackSpots(