We discuss the experimental procedure for extracting reliable phase information from a defocus series of transmission electron microscopy (TEM) dark-field images using the transport of intensity equation (TIE). Taking InGaN/GaN multi-quantum well light-emitting diode as a model system, various factors affecting the final result of reconstructed phase such as TEM sample preparation, TEM imaging condition, image alignment, the correction of defocus values and the use of high frequency pass filter are evaluated. The obtained phase of wave function was converted to the geometric phase of the corresponding lattice planes, which was then used for the two-dimensional mapping of lattice strain following the dark-field inline holography (DIH) routine. The strain map obtained by DIH after optimized image processing is compared with that obtained by the geometric phase analysis of high resolution TEM (HRTEM) image, manifesting that DIH yields more accurate and reliable strain information than HRTEM-based GPA.