Automate CP on single computer

I am trying to help a friend out with CellProfiler, so I do not have access to the images or pipeline and .mat file yet.

Basically, she uses CP to perform a pipeline of around 12 modules on 4 images: Red, Green, Blue, and DIC. The problem is, she wants to do this 1,000 times. So 1,000 sets of 4 images. We’re trying to figure out how to automate this on her laptop. We do NOT have access to a cluster. I found this thread in the forum: … ?f=2&t=743

Basically, the thread makes me think that we should be executing the pipeline in a loop with either a shell script or a MatLab routine. Then, the file names of the images could be entered via a list or we’d change their names so that they’re enumerated in a way that would allow the loop to pass each set of 4 to the pipeline.

I have limited experience with CP, but I was wondering if instead of this approach we could create batch files, and then somehow execute those automatically on her laptop.

What is the best and easiest option? Thanks.


Hmm, this sounds like a normal case of CP use. The pipeline is run once per image set (4 images in this case), so the looping is inherent in LoadImages. Or am I misunderstanding?

The thread you cite is for running the in an environment where you don’t want (or can’t run) the GUI. But that doesn’t sound like your problem, I think?


David, thanks for the quick reply.

I didn’t know that LoadImages would automate sets of multiple images. In our experience it would analyze 1,000 separate images in series, but we didn’t know how to do this with 1,000 sets of 4 images, one after the other.

I thought that we could run CellProfiler in a headless command-line mode in order to put the running of the pipeline in a for-loop. That way, we could repeat the 4-image analysis one after the other.

But it sounds like LoadImages was designed to do this, so I’ll try again. Thanks again!