Actually, hkl plane indices is indexed according to the crystal coordinate system and it has nothing to do with the setting Cartesian reference system. However, when you try to calculate plane spacing easily, it is needed to set up a Cartesian reference system. For consisting index for series TEM SAED images, stereo graphic projection would be helpful.
Ref. (1) Marc De Graef's TEM book, Introduction to Conventional Transmission Electron Microscopy
(2) Stereo graphic projection and simple electron diffraction simulation software PTCLab: http://sourceforge.net/projects/tclab