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
