コード例 #1
0
def save_qc_image(imp, rois, output_path):
    """save rois overlaid on imp to output_path"""
    imp.killRoi()
    roim = RoiManager(False)
    for roi in rois:
        roim.addRoi(roi)
    roim.runCommand("Show All with labels")
    RGBStackConverter.convertToRGB(imp)
    roim.moveRoisToOverlay(imp)
    FileSaver(imp).saveAsTiff(output_path)
    roim.runCommand("Show None")
    roim.close()
コード例 #2
0
def segmentation(imp, spot_data, channel, diameter_init, ES_tolerance, ES_area_max, ES_ctrl_pts, ES_iteration, repeat_max):
    # Open files
    cal = imp.getCalibration()
    manager = RoiManager.getInstance()
    if manager is None:
        manager = RoiManager()
    # Prepare log files for output
    options = IS.MEDIAN | IS.AREA | IS.MIN_MAX | IS.CENTROID | IS.PERIMETER | IS.ELLIPSE | IS.SKEWNESS
    convergence = []
    Sintensity = []
    for spot in spot_data:
        repeat = 0
        flag = False
        spotID = int(spot[0])
        Xcenter = (float(spot[1]) / cal.pixelWidth)
        Ycenter = (float(spot[2]) / cal.pixelHeight)
        Quality = float(spot[3])
        diameter_init = float(spot[4] / cal.pixelWidth) * 2.0
        while True:
            manager = RoiManager.getInstance()
            if manager is None:
                manager = RoiManager()
            Xcurrent = int(Xcenter - diameter_init / 2.0)
            Ycurrent = int(Ycenter - diameter_init / 2.0)
            Dcurrent1 = int(diameter_init * (1.2 - repeat / 10.0))
            Dcurrent2 = int(diameter_init * (0.8 + repeat / 10.0))
            roi = OvalRoi(Xcurrent, Ycurrent, Dcurrent1, Dcurrent2)
            imp.setPosition(channel)
            imp.setRoi(roi)
            Esnake_options1 = "target_brightness=Bright control_points=" + \
                str(ES_ctrl_pts) + " gaussian_blur=0 "
            Esnake_options2 = "energy_type=Contour alpha=2.0E-5 max_iterations=" + \
                str(ES_iteration) + " immortal=false"
            IJ.run(imp, "E-Snake", Esnake_options1 + Esnake_options2)
            roi_snake = manager.getRoisAsArray()
            roi_ind = len(roi_snake) - 1
            stats = IS.getStatistics(
                imp.getProcessor(), options, imp.getCalibration())
            perimeter = roi_snake[roi_ind].getLength() * cal.pixelWidth
            circularity = 4.0 * 3.1417 * (stats.area / (perimeter * perimeter))
            if stats.area > 17.0 and stats.area < ES_area_max and stats.skewness < -0.01 and circularity > 0.01 and stats.minor > 2.0 and boundaries(Xcenter, Ycenter, stats.xCentroid / cal.pixelWidth, stats.yCentroid / cal.pixelHeight, ES_tolerance):
                Sintensity = stats.median
                convergence.append(True)
                break
            if stats.median > 6000 and stats.area > 17.0 and stats.area < ES_area_max:
                Sintensity = stats.median
                convergence.append(True)
                break
            elif repeat > repeat_max:
                manager.select(imp, roi_ind)
                manager.runCommand(imp, 'Delete')
                roi = OvalRoi(Xcenter + 1.0 - diameter_init / 2.0, Ycenter +
                              1.0 - diameter_init / 2.0, diameter_init, diameter_init)
                imp.setRoi(roi)
                manager.add(imp, roi, spotID)
                roi_snake.append(roi)
                stats = IS.getStatistics(
                    imp.getProcessor(), options, imp.getCalibration())
                Sintensity = stats.median
                convergence.append(False)
                break
            else:
                IJ.log('Area=' + str(stats.area) + '  Skewness=' + str(stats.skewness) +
                       ' circularity=' + str(circularity) + ' Minor=' + str(stats.minor))
                manager.select(imp, roi_ind)
                manager.runCommand(imp, 'Delete')
                repeat += 1
        # End Spot-segmentation
    # End all Spots-segmentation
    manager.runCommand(imp, 'Show All')
    imp.setPosition(channel)
    color = imp.createImagePlus()
    ip = imp.getProcessor().duplicate()
    color.setProcessor("segmentation" + str(channel), ip)
    color.show()
    IJ.selectWindow("segmentation" + str(channel))
    manager.moveRoisToOverlay(color)
    spot_optimal = manager.getRoisAsArray()
    manager.reset()
    for i in xrange(0, len(spot_optimal)):
        spot = spot_optimal[i]
        spot.setStrokeWidth(2)
        if convergence[i]:
            spot.setStrokeColor(Color.GREEN)
        else:
            spot.setStrokeColor(Color.MAGENTA)
        imp.setRoi(spot)
        manager.add(imp, spot, i)
    manager.runCommand(imp, 'Show All')
    imp.setPosition(channel)
コード例 #3
0
def Overlayer(org_size, dirs):
	""" Overlays ROIs with appropriate color,
	    saves to .tif and animates aligned images to .gif """
    
    # Get colors.
	Colors, Colors_old = colorlist()

    # Get ROImanager.
	rm = RoiManager().getInstance()
	rois = rm.getCount()
	
	# Overlays ROI on aligned images, converts to 8-bit (for gif).
	for root, directories, filenames in os.walk(dirs["Composites_Aligned"]):
		for filename in filenames:
			imp = IJ.openImage(os.path.join(root, filename))
			converter = ImageConverter(imp)
			converter.setDoScaling(True)
			converter.convertToGray8()

			# Lookup table and local contrast enhancement for vizualisation.
			IJ.run(imp, "Rainbow RGB", "")
			IJ.run(imp, "Enhance Local Contrast (CLAHE)", 
			       "blocksize=127 histogram=256 maximum=3 mask=*None*")

			
			for roi in range(rois):
				roi_obj = rm.getRoi(roi)
				roi_obj.setStrokeWidth(2)		
				if roi < 19:
					roi_obj.setStrokeColor(Color(*Colors[roi][0:3]))
				else:
					roi_obj.setStrokeColor(eval(Colors_old[roi]))
			
			
			rm.moveRoisToOverlay(imp)

			IJ.saveAs(imp, "Tiff", os.path.join(dirs["Overlays"], filename))
			
	# Opens overlaid images, saves as tiff stack.
	overlay_stack = IJ.run("Image Sequence...", "open="+dirs["Overlays"]+
					       " number=3040 starting=0 increment=1 scale=300 file=.tif sort")
	
	# Takes care of spaces in titles. 
	tiftitle = Title.replace(" ", "_")
	tiftitle = tiftitle.replace(".", "_")
	
	# Gets dimensions for scalebar.
	imp = WindowManager.getImage("Overlays")
	dimensions = imp.getDimensions()
	size = dimensions[0] + dimensions[1]
	microns = org_size / size

	# Sets scale and writes scale-bar, flattens overlays. 
	IJ.run(imp, "Set Scale...", "distance=1 known="
	       +str(microns)+" pixel=1 unit=micron")
           
	IJ.run(imp, "Scale Bar...", 
	    "width=10 height=4 font=14 color=Yellow background=None location=[Lower Right] bold overlay")
    
	IJ.run(imp, "Flatten", "stack")
	IJ.saveAs(imp, "Tiff", os.path.join(dirs["Gifs"], tiftitle))
	
	# Animates tiff stack from directoy. 
	for root, directories, filenames in os.walk(dirs["Gifs"]):
		for filename in filenames:		
			if tiftitle in filename and filename.endswith(".tif"):
				# set=xx parameter controls gif speed.
				# for additional parameters run with macro recorder.
				try:
					print "Animating gif..."
					imp = WindowManager.getImage(tiftitle + ".tif")
					gif = IJ.run("Animated Gif ... ", 
					             "set=200 number=0 filename="
					             + os.path.join(dirs["Gifs"], tiftitle + ".gif"))
				
				except Exception, e:
					print str(e)
				
				print "gif animated."