pythin_imageJ

import os
import fijibin
import fijibin.macro
import subprocess

path_to_imageJ = os.path.join(os.getcwd(), "Application\\Fiji.app\\ImageJ-win64.exe")  # Location of ImageJ
path_to_file = os.path.join(os.getcwd(), "clown1.jpg")  # Location of the first image file of my sequence
x = 100  # Variable distance value
y = 543  # Variable known value

macro_single_file = """ run("Open...");
run("Image Sequence...", "open=[path_to_file] sort");
run("Set Scale...", "distance=x known=y unit=microns"); """

subprocess.call([path_to_imageJ])  # This successfully opens the imageJ GUI
fijibin.macro.run(macro_single_file)  # This should ideally run my macro in the loaded GUI above

# As per the suggested links, I can also run the commands in terminal by using
# os.system('dir')
#                            --or--
# proc = subprocess.Popen('cmd.exe', stdin = subprocess.PIPE, stdout = subprocess.PIPE)
# stdout, stderr = proc.communicate(b'dir c:\\')
# print(stdout)