# Fetch an RGB image stack
imp_rgb = IJ.getImage() # IJ.openImage("http://imagej.nih.gov/ij/images/flybrain.zip")
# Define a threshold for the red channel: any values at or above
# in the green channel will be placed into a new image
threshold = 119
# Example 1: with ImageCalculator
from ij.process import ImageProcessor
from ij.plugin import ChannelSplitter, ImageCalculator
# Split color channels
red, green, blue = ChannelSplitter().split(imp_rgb) # 3 ImagePlus
# Set threshold for each slice
for index in xrange(1, red.getNSlices() + 1):
bp = red.getStack().getProcessor(index)
#bp.setThreshold(threshold, 255, ImageProcessor.BLACK_AND_WHITE_LUT)
bp.threshold(threshold) # mask is 0, background is 255
# Apply threshold: convert each slice to a mask (only 0 or 255 pixel values)
#IJ.run(red, "Convert to Mask", "method=Default background=Dark black")
red.show()
green_under_red_mask = ImageCalculator().run("and create stack", red, green)
green_under_red_mask.show()
"""
# Example 2: with ImgLib2 LoopBuilder
from net.imglib2.img.display.imagej import ImageJFunctions as IL
from net.imglib2.converter import Converters
