Run Cellprofiler pipeline from a GUI in Matlab

cellprofiler

#1

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?


#2

Ah, flashbacks of a few years ago when CellProfiler was written in Matlab! :smile:

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?
Cheers,
David


#3

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.)

System:
Mac OSX 10.13.2 High Sierra
Matlab R2017b
Python 2.6
CellProfiler 3.0.0rc7

Any guidance is much appreciated! Thank you!

-Sarah


#4

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.