imgpath = '/Volumes/D/Julia20130201-/almfscreen/samples_112712/l5/l5c1.tif' imp = IJ.openImage(imgpath) ntd = NucToDots(imp); ntd.run() # runs CLAHE first, takes a bit of time. #ntd.runmain() # for imp that is already stackCLAHEed. #for i in ntd.getXcoordA(): # print i print "Extracting Nucleus ..." subwwhh = 130 # this must be guessed in the pre-run, by doing particle analysis and get the approximate sizes. WATERSHED_THRESHOLD = 0.10; en = NucleusExtractor(imp, ntd.getXcoordA(), ntd.getYcoordA(), ntd.getFrameA()) en.constructNodesByDots(subwwhh, WATERSHED_THRESHOLD) print 'node length before filtering: ' + str(en.getNodes().size()) en.analyzeDotsandBinImages() print 'node length after filtering: ' + str(en.getNodes().size()) nodes = en.getNodes() ''' stk = ImageStack(subwwhh, subwwhh) for n in nodes: binip = n.getBinip() stk.addSlice(binip) ImagePlus("tt", stk).show() ''' IJ.log('Linking ...')
ntd = NucToDots(imp); ntd.run() subwwhh = 120 # size of sub image # from here is the extraction ''' nrp = NRP() nrp.getPerNucleusBinImgProcessors(imp, subwwhh, ntd.getXcoordA(), ntd.getYcoordA(), ntd.getFrameA()) stk = nrp.getBinStack(); ''' en = NucleusExtractor(imp, ntd.getXcoordA(), ntd.getYcoordA(), ntd.getFrameA()) en.constructNodes(subwwhh) en.analyzeDotsandBinImages() nodes = en.getNodes() stk = ImageStack(subwwhh, subwwhh) for n in nodes: binip = n.getBinip() stk.addSlice(binip) ''' stk = ImageStack(subwwhh, subwwhh) for i, f in enumerate(ntd.getFrameA()): ip = imp.getStack().getProcessor(f) roi = nrp.makeRoi(ip, ntd.getXcoordA()[i], ntd.getYcoordA()[i], subwwhh, subwwhh) subip = nrp.extract(ip, roi) binip = nrp.binarize(subip) stk.addSlice(binip) ''' ImagePlus("res", stk).show()