print 'No cell ROI on slice ' + str(zslice) impBin1.changes = False impBin1.close() continue #Get nuclei ROIs ip2 = nucleistack.getProcessor(zslice) ip2.resetMinAndMax() ip2.blurGaussian(parameters['nucsigma']) bp2 = ip2.convertToByte(1) impBin2 = ImagePlus('BinarizedNuclei', bp2) impBin2.show() rmi.select(impBin2, rmi.getCount() - 1) IJ.setBackgroundColor(0, 0, 0) IJ.run('Clear Outside') impBin2.deleteRoi() IJ.selectWindow('BinarizedNuclei') IJ.run('Auto Threshold', 'method=' + parameters['nucmethod'] + ' ignore_black white') #threshold the template region IJ.run('Watershed') #Remove template ROI rmi.reset() impBin2.killRoi() #Add nuclei to ROIs IJ.run( 'Analyze Particles...', 'size=' + parameters['nucsize'] + ' circularity=' + parameters['nuccircularity'] + ' exclude add') rois.append([zslice, rmi.getRoisAsArray()]) print 'Added ' + str(len(rmi.getRoisAsArray())) + ' ROIs' #Close images