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Created March 25, 2014 16:15
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import os, sys
from ij.plugin.filter import ParticleAnalyzer as PA
# size of juxtanuclear region. In pixels.
RIMSIZE = 15
def roiRingGenerator(r1):
""" Create a band of ROI outside the argument ROI.
See Liebel (2003) Fig. 1
"""
#r1 = imp.getRoi()
r2 = RoiEnlarger.enlarge(r1, RIMSIZE)
sr1 = ShapeRoi(r1)
sr2 = ShapeRoi(r2)
return sr2.not(sr1)
def roiEnlarger(r1):
""" Enlarges ROI by a defined iterations.
"""
return ShapeRoi(RoiEnlarger.enlarge(r1, RIMSIZE))
def measureROIs(imp, measOpt, thisrt, roiA, backint, doGLCM):
""" Cell-wise measurment using ROI array.
"""
analObj = Analyzer(imp, measOpt, thisrt)
for index, r in enumerate(roiA):
imp.deleteRoi()
imp.setRoi(r)
analObj.measure()
maxint = thisrt.getValue('Max', thisrt.getCounter()-1)
saturation = 0
if ( maxint + backint) >= 4095:
saturation = 1
if (VERBOSE):
print 'cell index ', index, 'maxint=', maxint
thisrt.setValue('CellIndex', thisrt.getCounter()-1, index)
thisrt.setValue('Saturation', thisrt.getCounter()-1, saturation)
if (doGLCM):
imp.deleteRoi()
#measureTexture(imp, thisrt, roiA)
## loading files
root = '/Volumes/data/bio-it_centres_course/data/course'
fileNuc = 'dapiSegmented.tif'
filepm = 'pm-647BackSub.tif'
filevsvg = 'vsvg-cfpBackSub.tif'
nucfull = os.path.join(root, fileNuc)
pmfull = os.path.join(root, filepm)
vsvgfull = os.path.join(root, filevsvg)
impfilteredNuc = IJ.openImage(nucfull)
impPM = IJ.openImage(pmfull)
impVSVG = IJ.openImage(vsvgfull)
wnumber = '00005'
rtallcellPM = ResultsTable()
rtjnucVSVG = ResultsTable()
rtallcellVSVG = ResultsTable()
intmax = impfilteredNuc.getProcessor().getMax()
if intmax == 0:
#return rtallcellPM, rtjnucVSVG, rtallcellVSVG
exit()
impfilteredNuc.getProcessor().setThreshold(1, intmax, ImageProcessor.NO_LUT_UPDATE)
nucroi = ThresholdToSelection().convert(impfilteredNuc.getProcessor())
nucroiA = ShapeRoi(nucroi).getRois()
#print nucroiA
allcellA = [roiEnlarger(r) for r in nucroiA]
jnucroiA = [roiRingGenerator(r) for r in nucroiA]
measOpt = PA.AREA + PA.MEAN + PA.CENTROID + PA.STD_DEV + PA.SHAPE_DESCRIPTORS + PA.INTEGRATED_DENSITY + PA.MIN_MAX +\
PA.SKEWNESS + PA.KURTOSIS + PA.MEDIAN + PA.MODE
## All Cell Plasma Membrane intensity
measureROIs(impPM, measOpt, rtallcellPM, allcellA, 0, True)
meanInt_Cell = rtallcellPM.getColumn(rtallcellPM.getColumnIndex('Mean'))
print "Results Table rownumber:", len(meanInt_Cell)
# JuxtaNuclear VSVG intensity
measureROIs(impVSVG, measOpt, rtjnucVSVG, jnucroiA, 0, False)
meanInt_jnuc = rtjnucVSVG.getColumn(rtjnucVSVG.getColumnIndex('Mean'))
# AllCell VSVG intensity
measureROIs(impVSVG, measOpt, rtallcellVSVG, allcellA, 0, True)
meanInt_vsvgall = rtallcellVSVG.getColumn(rtallcellVSVG.getColumnIndex('Mean'))
for i in range(len(meanInt_Cell)):
if meanInt_Cell[i] != 0.0:
transportR = meanInt_jnuc[i] / meanInt_Cell[i]
transportRall = meanInt_vsvgall[i] / meanInt_Cell[i]
else:
transportR = float('inf')
transportRall = float('inf')
rtjnucVSVG.setValue('TransportRatio', i, transportR)
rtallcellVSVG.setValue('TransportRatio', i, transportRall)
rtjnucVSVG.setValue('WellNumber', i, int(wnumber))
rtallcellVSVG.setValue('WellNumber', i, int(wnumber))
rtallcellPM.setValue('WellNumber', i, int(wnumber))
rtallcellVSVG.show('AllCell')
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