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 ...') dlh = DLH(imp, 3, 10) # linkrange, distance