from ij import IJ, ImagePlus
from java.lang import Runtime, Runnable

import os

filepaths = []

for folder, subs, files in os.walk('location/of/files/'):
    for filename in files:
        #the next part stops it appending DS files
        if not filename.startswith('.'):
            filepaths.append(os.path.abspath(os.path.join(folder, filename,)))

for i in filepaths:
    IJ.open(i);
    IJ.close();