Sequential batch processing



The images that I want to analyze with CellProfiler are located in a folder structure as follows: A main data folder containing several subfolders containing each the images of a set. (One set of images has the size of around 2000 images).

Now I would like to process the subfolders in batches (one subfolder per batch), but not in parallel but sequentially and receive for each subfolder a separate output file (e.g. DefaultOUT1, DefaultOUT2, etc.) Is there a module with which I can do this other than starting the analysis for each subfolder manually?

I am grateful for help

Best, Martin


Hi Martin,

Currently, CellProfiler does not have the ability to batch process directories in this manner, although we are in the process of adding that functionality.

In the meantime, you may want to try running “Run Multiple Pipelines” from the “File” menu on the taskbar. This function will ask you to specify a root directory, and will then give you all pipelines in all subdirectories under that root. After selecting which pipelines you want to run, it will switch to the directory which each pipeline is located in turn and run it, with the DefaultOUT file saved to the directory where the pipeline was located.

So if (1) your images are placed in subfolders under a root directory, and (2) you place a copy of your pipeline in each directory, and use “Run Multiple Pipelines,” it should approximate the behavior you want.



Hi Mark,

I am happy to hear that the functionality of batch processing directories will be added to CellProfiler in the future. At the moment I do it as you mentioned above and this works just fine for now.

Thank you very much for your help-
Best, Martin