Integrate R into PickCells


Hi all,

This is a poll to probe whether people think that integrating R into PickCells maybe useful. Personally I think this would be a formidable addition. As you know R is widely adopted as a powerful data mining and graphics tool. Currently PickCells allow you to export your data in table formats which can then be imported into R. This forces you to perform the transfer manually, which is fine (although this might be repetitive and tedious) but the problem is that there is no way to import classifications performed by R back into PickCells to be used for other purposes such as visualising classified cells in images or 3D views for example.

In practice PickCells users will be able to open an R prompt from within PickCells and use PickCells graphical query builders to create data frames in R. These data frames will keep track of the type of objects they are (nucleus, colony …) so that any (allowed) modification performed in R can be reflected into the PickCells database once modifications are validated.

##Would you like to see R integrated into PickCells?##
(1 is ‘I won’t use it’ 5 is ’ definitely yes’)

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0 voters

Any comment or suggestion, do not hesitate to reply to this post!



I think this would be a really good idea.
Something that came to my mind was the JGR (Java GUI for R) , maybe it’s worth taking a look :panda_face:


Thanks very much for the links @SamW!
I also found this thread which maybe useful. The great thing is that PickCells already include an rJava module which could be extended for this feature.


I really like the idea, but it would be great to have both options available (using R and exporting to do your own analysis using other software).