Cell Painting: Establishing the platform (2)

This is the second question regarding the establishment of the Cell Painting platform (original post at Cell Painting: Establishing the platform) This is regarding CellProfiler:
Would it be preferred to use CellProfiler 3.x (eg. 3.1.5) to analyse the images? Since the raw image data is available from your previous work (Bray et al 2017), we have the option to analyse the data that we would like to compare with (compounds with known MoA) in the newest CellProfiler version. We can then use the new version for our own data.
Or is it simply more reliable to use CellProfiler version 2.1.1/2.2.0 as has been used in the previous papers (Bray et al 2017, Bray et al 2016) for our own data, and then compare directly to the profiles generated in the above mentioned papers?

With Kind Regards
Esben B. Svenningsen, Ph.D. Student
Aarhus University, Denmark
Department of Chemistry, Thomas B. Poulsen

Bray, M. A. et al, Gigascience, 2017, 6, 1–5.
Bray, M. A. et al, Nat. Protoc., 2016, 11, 1757–1774.