Run Cellprofiler pipeline from a GUI in Matlab


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! :smile:

You can run CP from the command line: … 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
Matlab R2017b
Python 2.6
CellProfiler 3.0.0rc7

Any guidance is much appreciated! Thank you!



Hi Sarah,

I’m not a matlab expert at all, but if you pass CP headless commands with the switches found here you should be able to run it on a particular pipeline and set of images that way.