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| from fiji.threshold import Auto_Local_Threshold as ALT | |
| # nucleus selection | |
| #imp = IJ.getImage() | |
| imp = IJ.openImage("/Users/miyanari/Desktop/EMBL_with Kota/FISH_data/DNA-FISH_Demo.tif") | |
| #IJ.run(imp, "Split Channels", "") | |
| imps = ChannelSplitter.split(imp) | |
| nucimp = imps[0] | |
| #nucimp.show() | |
| #Z projection | |
| zpnuc = ZProjector(nucimp) | |
| zpnuc.setMethod(ZProjector.MAX_METHOD) | |
| zpnuc.doProjection() | |
| zpnucimp = zpnuc.getProjection() | |
| zpnucimp.show() | |
| #Gaussian blur | |
| gbnuc = GaussianBlur() | |
| ip = zpnucimp.getProcessor() | |
| gbnuc.blurGaussian(ip, 3, 3, 0.01) | |
| #Auto local threshold | |
| #IJ.run(imp, "Auto Local Threshold", "method=Bernsen radius=45 parameter_1=0 parameter_2=0 white"); | |
| ALT().exec(zpnucimp, "Niblack", 30, 0, 0, True) | |
| #print len(thimp) | |
| #imps[0].show() | |
| #thimp.show() | |
| #thimp[0].show() | |
| #analyze particle | |
| rt = ResultsTable() | |
| measopt = ParticleAnalyzer.AREA + ParticleAnalyzer.SHAPE_DESCRIPTORS | |
| paopt = ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES | |
| paopt += ParticleAnalyzer.INCLUDE_HOLES | |
| paopt += ParticleAnalyzer.SHOW_MASKS | |
| paopt += ParticleAnalyzer.CLEAR_WORKSHEET | |
| paopt += ParticleAnalyzer.SHOW_RESULTS | |
| apnuc = ParticleAnalyzer(paopt, measopt, rt, 3000, 40000000, 0.6, 1.0) | |
| apnuc.analyze(zpnucimp) | |
| maskimp = apnuc.getOutputImage() | |
| maskimp.show() | |
| maskimp.close() |
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