Thanks for helping me submit bug. From your test, it seems that more data obtained from Mac OS is not aligned. I agree with you that those misaligned data does not seem to be made on objects that should be discarded.
My original intention is to discard secondary objects that touch the image border and not to include any objects whose AreaShape_Area is 0 or NaN. But due to my mistake, I got a lot of unaligned data like zipped package 1-test(1-test.zip (2.5 MB) ) which took me weeks to get it.
From my test, I think the data (2-test.zip (2.4 MB)) obtained by choosing discard secondary objects that touch the image border and discard the associated primary object is aligned as expected. I find when the imagenumber is the same, the cell BQ2:DP51 in Table 1-analysis_Per_CytoplasmMito (1-test.zip) corresponds to the cell BQ2:DP51 in Table 2-analysis_Per_CytoplasmMito (2-test.zip).
Therefore, taking the BQ column (CytoplasmMito_Texture_AngularSecondMoment_OrigMito_8_00) in Table 1-analysis_Per_CytoplasmMito as an example, I think the data in cell BQ2 should actually be measured by CytoplasmMito_Number_Object_Number 5 in ImageNumber 1 according to CytoplasmMito_Parent_Nuclei number.
By analogy, I may be able to know the actual order of unaligned data and write a simple script to align the data. But I need to further confirm my hypothesis from the source code. However, I am not familiar with the CellProfiler source code and I am not good at programming. Checking the source code is too difficult for me. So I hope your team can help me check the source code in the new year so that I can remedy my data.
Merry Christmas in advance