Suggestion for track measurements export

cellprofiler

#1

Hi,

First, thanks for this very powerful software!

I have a simple suggestion with regards to the tracking module. When the measurements are exported, the columns label are: {measurement}_{maximum distance}. I would suggest to remove the _{maximum distance}, because it disrupts the automated analysis one might programs, since the labels of the spreadsheets columns can change between different experiments. So one has to take this into account for each experiment one runs. If one would like to retrieve the maximum distance they use for the tracking, there must be a more efficient way than putting the information in a column label (such as a info.txt file).

Thanks,
Arthur


#2

Hi Arthur,

Thanks for the suggestion! The reason we put that {maximum distance} number in the column is to distinguish it if one might use multiple TrackObjects modules with different {maximum distance} threshold values. We can’t assume a user only has one TrackObjects module, though in the majority of cases this would certainly be true. I agree that these sorts of metadata should be stored in a more efficient, useful way, as in a relational database.

But other modules use this scheme too that have particular scale parameters that differ between instances (e.g. MeasureObjectNeighbors, MeasureImageQuality) and so any change we make should be done carefully.Another consideration is that any change we make to the measurement names would cause back-compatibility issues, and complicate any post hoc analyses as you are describing!

I added a Github issue feature request, though I suspect that changing your post hoc analyses to take into account the scale parameter at the end of the column name will be the most efficient solution, sorry.

Thanks,
David


#3

Hi Arthur,
We decided against the change, you can see our discussion here: github.com/CellProfiler/CellPro … ssues/1682

But feel free to further argue your case if you think it warranted!
Anne


#4

Thanks for your answers. Your choice seems legitimate then.