2 possible updates


Let me know whether this is the correct forum to give ideas for future updates.

It would be very nice to have kind of a “checkbox” for each module in the pipleline to enable/disable it. It is much faster than adding/removing and could keep the parameters (instead of manually adding them again).

Another useful idea could be another checkbox for each module to decide if we want to plot or not the results. I know the option in File-> Set preferences, but that is for the whole pipeline, and not for specific modules.

I hope you consider my comments interesting.




You can post ideas here or in the “New Modules” forum, which I should probably rename to “New Ideas”.

We recently released a new version of CellProfiler last week, and this version already has the ability to open only specified module windows. If you set this preference in the Set Preferences window to “Specify Windows To Display”, when you click “Analyze Images”, a window will open listing all of the modules in your pipeline and a checkbox. You can then decide which ones to open.

I think the enabling and disabling of modules in a similar fashion is a great idea. We always take users suggestions in to consideration and if feasible we implement these ideas as soon as possible.



Are there any updates on this topic? I just got the same ideatoday and realized I am 2 years late… :slight_smile:


The second idea of enabling/disabling each individual module’s plot was implemented long ago (look in Set Preferences for the setting), but the first suggestion of requesting selective disabling of an entire module has not. This would require downstream modules to be aware of which modules were active, and changing some of their settings accordingly. We understand the benefit of this to the user, as well as other pluses, like contextual settings (e.g. graying out of settings depending on other settings), but since it is a fairly major overhaul, it is not on our short term ToDo list. But thanks for the reminder!



I found the option in the set preferences menu. Here, I can check which windows should pop up during the run, but I have to do this everytime I start a run. Would it be possible to add a button that would remember the last settings for the pipeline?


A suggestion to the problem that David outlined two posts above: Would it be possible to put a checkbox that would enable to run stop the run at that point.
Or is that what can be done by adding “PauseCellProfiler”?


That’s precisely what PauseCellProfiler does. It then gives you the option of halting execution or continuing the run. I’ve ended up using it quite a bit while debugging multi-cycle pipelines.


And your suggestion to “remember the last [window display] settings for the pipeline” is a good one, and has been on our ToDo list.