from ij import IJ, WindowManager
from ij.plugin.frame import RoiManager
from ij.plugin import ChannelSplitter, Thresholder
from ij.plugin.filter import ParticleAnalyzer
from ij.io import FileSaver
import time, sys
imp = IJ.getImage()
csplitter = ChannelSplitter()
thresholder = Thresholder()
channels = csplitter.splitRGB(imp.getStack(), False)
blueImp = ImagePlus("blue", channels[2])
blueImp.getProcessor().invert()
blueImp.show()
WindowManager.setTempCurrentImage(blueImp)
IJ.run("Make Binary")
blueImp.hide()
roim = RoiManager(True)
# Create a ParticleAnalyzer, with arguments:
# 1. options (could be SHOW_ROI_MASKS, SHOW_OUTLINES, SHOW_MASKS, SHOW_NONE, ADD_TO_MANAGER, and others; combined with bitwise-or)
# 2. measurement options (see [http://rsb.info.nih.gov/ij/developer/api/ij/measure/Measurements.html Measurements])
# 3. a ResultsTable to store the measurements
# 4,5. The min and max size of a particle to consider for measurement
# 6,7. The min and max circularity (values between 0 and 1 perfect circle)
pa = ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER, Measurements.AREA, None,
200, 4000, 0.4, 1.0)
pa.setHideOutputImage(True)
