Selection in CellProfiler Analyst



I saw this functionality on an older tutorial for CellProfiler Analyst: a selection was made in one scatter plot, and the cells that it selected were highlighted in another scatter plot.
I can’t seem to get the selection to work at all. By default my clicking and dragging motion does nothing to the scatter plot. I’ve made sure both the zoom and panner modes are deselected. Shift clicking, alt clicking, nothing seems to create a selection.
Am I missing something, or did maybe the functionality change between versions or something? Any help would be much appreciated. Thank you.


The selection functions are currently being affected by a bug and therefore aren’t turned on in 2.2.


Oh dang, any idea when this functionality might be back? It’s really useful to be able to relate objects from one plot of certain data, to another plot of different data.


I don’t, sorry- the best way to demonstrate that people need that feature is to make a GitHub account, go to the CPA issues forum, and ask for it.

In the meantime, as a workaround, you can create a gate in one scatter plot and then apply that gate as a filter in a second plot- it won’t highlight the ones that are in vs out of the gate, but it will allow you to look just at that subpopulation.


Okay, maybe I will try that.

Also, thank you, I was aware of this functionality. It doesn’t quite solve my problem though, because what I really want to do is highlight various cell population types, based on certain values, and then see where they relate to one another in a spatial context. Kind of trying to see if their local environment may be influencing the cell fate they become.


I know it’s not a perfect solution, it’s just the one I could think of.

I’m thinking you might also want to try using the Data Tools built into CellProfiler itself- if you run (or rerun) your pipeline such that it creates a .mat or a .h5 file at the end, you can then load that into Data Tools and you can at least do things like display the values from your various objects on top of your image so that you can get an idea of the spatial relationship.


I was actually planning on working with the csv I get from the ExportToSpreadsheet module and creating the plots that way.
Thank you though.