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: cellprofiler.org/forum/viewt … ?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.