"brush" function gone and processing speed issue

Hi there,

CP and CPA are really invaluable tools. I realize now that CPA is actually utterly important, since while CP is great to produce data, what is the point if you cannot easily process that data? It is really too bad you did not get support to keep on improving CPA. Anyway…
I understand the “Brushing” originally described in your 2008 paper in Bioinformatics is not functional in CPA2 anymore (?!). I tried the “double lasso” strategy to select cells on a dot-plot in CPA2, which works fine, but VERY slowly. I have about 200000 cells, single channel, in a SQLite base (70Mo), on a W7 PC dual core 2.4GHz, 18Go RAM.
My questions:

  • Is it normal that it is so slow (>15s before anything shows up)?
  • When I do lasso-select some cells in a dot-plot, nothing happens in the other dot-plots/histograms already opened, nor in newly created ones. What should I do to get the convenience of the brushing you originally described?

Thanks for your help, and these great programs!

Hi,
Sorry to say our support for CPA is lacking (and slow!) I suspect the brushing functionality you’re looking for is only available in the older version of CPA - have you tried that?
Anne

[quote=“Anne Carpenter”]Hi,
Sorry to say our support for CPA is lacking (and slow!) I suspect the brushing functionality you’re looking for is only available in the older version of CPA - have you tried that?
Anne[/quote]

Thak you Anne for your time. I must say I haven’t tried the older CDA version. Wouldn’t that be a regression?? It is really too bad you guys don’t have the possibility to develop CPA anymore. What is the point of recording a nice piece of music (CP) if one does not have a good player (CPA) to listen to it?

We re-wrote CPA from scratch, in Python instead of Java, in order to give it more sophisticated capabilities overall. It resulted in a much nicer piece of software overall and we have since added many new features, but the brushing functionality was (I think) one feature that was not re-instituted in the new CPA 2.0, as it was less popular. We continue to maintain CPA 2.0 and especially develop its machine learning capabilities.

Feel free to lobby Congress and the NIH to devote more financial support for software projects. And, encourage those who review papers and grants to advocate for the impact of software-related work. In the meantime, I’m happy to offer you a full refund. :smile:

You can download old versions of CPA here:
cellprofiler.org/previousReleasesCPA.shtml