  We explore data reduction and correction steps and processed data
reproducibility in the emerging single crystal total scattering based technique
of three-dimensional differential atomic pair distribution function
(3D-$\Delta$PDF) analysis. All steps from sample measurement to data-processing
are outlined in detail using a CuIr$_2$S$_4$ example crystal studied in a setup
equipped with a high-energy x-ray beam and a flat panel area detector.
Computational overhead as it pertains to data-sampling and the associated data
processing steps is also discussed. Various aspects of the final 3D-$\Delta$PDF
reproducibility are explicitly tested by varying data-processing order and
included steps, and by carrying out a crystal-to-crystal data comparison. We
identify situations in which the 3D-$\Delta$PDF is robust, and caution against
a few particular cases which can lead to inconsistent 3D-$\Delta$PDFs. Although
not all the approaches applied here-in will be valid across all systems, and a
more in-depth analysis of some of the effects of the data processing steps may
still needed, the methods collected here-in represent the start of a more
systematic discussion about data processing and corrections in this field.
