def make_outline_image(imp):
imp.show() # one needs to display it, otherwise below function cannot find it
IJ.run("3D Fast Filters","filter=Minimum radius_x_pix=1.0 radius_y_pix=1.0 radius_z_pix=1.0");
imp.hide()
imp_minimum = WindowManager.getImage("3D_Minimum")
imp_outlines = imp.duplicate()
calc = ImageCalculator()
calc.calculate("Subtract stack", imp_outlines, imp_minimum)
# clean up
imp_minimum.close()
imp_outlines.setTitle("Outlines")
return imp_outlines
from ij import IJ # imports the IJ class
from ij.plugin import ImageCalculator # imports the Image Calculator from the ImageJ Plugins
imp = IJ.getImage() # gets the title of the image
IJ.run(imp, "Duplicate...",
"title=duplicate.tif duplicate") # runs duplication on selected image
imp_2 = IJ.getImage() # gets title of duplicated image
IJ.run(imp, "Gaussian Blur 3D...", "x=2 y=2 z=2")
# runs gaussian blur 3D on original image
IJ.run(imp_2, "Gaussian Blur 3D...", "x=4 y=4 z=4")
# runs gaussian blur 3D on duplicated image
calc = ImageCalculator() # setting the function equal to the variable calc
calc.calculate(
"Subtract create stack", imp,
imp_2) # calling the ImageCalculator() to subtract imp minus imp_2
imp.close() # closes original image
imp_2.close() # closes duplicate image
#print imp.title
IJ.run("Convert Stack to Images");
win = w.getWindow("Blue")
win.removeNotify()
IJ.selectWindow("Red")
IJ.run("16-bit");
red=IJ.getImage()
IJ.selectWindow("Green")
IJ.run("16-bit")
green=IJ.getImage()
calc = ImageCalculator()
calc.calculate("Add create", red,green);
IJ.run("Subtract Background...", "rolling=50");
IJ.run("LoG 3D");
imp = IJ.getImage()
pix = imp.getProcessor().convertToFloat().getPixels()
# find out the minimal pixel value
min = reduce(Math.min, pix)
# create a new pixel array with the minimal value subtracted
pix2 = map(lambda x: x - min, pix)
name="log"
ImagePlus(name, FloatProcessor(imp.width, imp.height, pix2, None)).show()
