def getManders(self, imp, cell): ### Crop channels according to cell mask channels = self.getCroppedChannels(imp, cell) if channels is None: return None ### Calculate channel thresholds thrs = [] thrimps = [] for c, method in enumerate(self.methods): if method != "None": thr, thrimp = self.getThreshold(channels[c], method) else: thr, thrimp = None, None thrs.append(thr) thrimps.append(thrimp) ### Calculate manders colocalization manders = MandersColocalization() raws = [] thrds = [] for chA, chB in self.pairs: container = self.getContainer(channels[chA - 1], channels[chB - 1]) img1 = container.getSourceImage1() img2 = container.getSourceImage2() mask = container.getMask() cursor = TwinCursor(img1.randomAccess(), img2.randomAccess(), Views.iterable(mask).localizingCursor()) rtype = img1.randomAccess().get().createVariable() raw = manders.calculateMandersCorrelation(cursor, rtype) rthr1 = rtype.copy() rthr2 = rtype.copy() rthr1.set(thrs[chA - 1]) rthr2.set(thrs[chB - 1]) cursor.reset() thrd = manders.calculateMandersCorrelation(cursor, rthr1, rthr2, ThresholdMode.Above) raws.append(raw) thrds.append(thrd) return (channels, thrimps, thrs, raws, thrds)
projector = ZProjector()
splitter = ChannelSplitter()
imp1 = ImagePlus("CH1", )
width, height, channels, slices, frames = image.getDimensions()
chimps = []
for ch in range(1, channels + 1):
projector = ZProjector(ImagePlus("C%i" % ch, splitter.getChannel(image, ch)))
projector.setMethod(ZProjector.MAX_METHOD)
projector.doProjection()
proj = projector.getProjection()
enhancer.equalize(proj)
chimps.append(proj)
return RGBStackMerge.mergeChannels(chimps, False)
manders = MandersColocalization()
results = ResultsTable()
for imageFile in os.listdir(inputDir):
print "Opening " + imageFile
try:
images = BF.openImagePlus(inputDir + imageFile)
image = images[0]
except UnknownFormatException:
continue
preview = getPreview(image)
preview.show()
rm = RoiManager()
dialog = WaitForUserDialog("Action required", "Please select regions of interest in this image. Click OK when done.")
dialog.show()
rm.close()
splitter = ChannelSplitter()
