The goal is a Matlab GUI that can pass user-defined parameters for illumination correction functions into a Cellprofiler pipeline and display and evaluate interactively the outputs in the GUI. Does anyone know how to run a Cellprofiler pipeline from a Matlab GUI?
Ah, flashbacks of a few years ago when CellProfiler was written in Matlab!
You can run CP from the command line:
github.com/CellProfiler/CellPro … mmand_line
So in Matlab, you should be able to run the “system” command (or other similar ones) to execute CP, though I have not tested this for a long time.
Does that help?
Hi CP Team,
I’m very new to programming, so please forgive me for the basic questions. I was able to execute the System command in Matlab, and it brought up the CellProfiler application. However, I’m wondering if it is possible and how to run a pipeline in “headless mode” so that the pipeline executes automatically when I run my Matlab script. (I have a pipeline and an image I want it to be able to process that works in the application just fine.)
Mac OSX 10.13.2 High Sierra
Any guidance is much appreciated! Thank you!