Duplicating many modules / cppipe file editing?

Dear cellprofilers,

I need to use a pipeline where the same set of operations needs to be applied on different sets of images, (differing by exposure time, for instance).
Depending on the experiments, I will have 5 different exposures, or 10. This can vary, but many operations need to be applied identically.

So far, the way it’s done in the pipeline is by duplicating many times the same modules, changing the parameter for image name ‘image_exp3ms’, ‘image_exp10ms’, ‘image_exp20ms’, etc.

But obviously if I want to change a parameter (thresholding for instance), this means that I need to change it identically in all duplicated modules, which is tedious.

So, to improve this, my current plan is the following:

  • I write a cppipe file with a single and generic image_$exptime image name parameter
  • Then I export this pipeline as a .cppipe file
  • Finally I programmatically generate a new cppipe file which will duplicate all modules for as many time as needed
    ** by parsing the generic cppipe file:
    ** -> search for image_$exp parameter in modules
    ** -> then duplicating module as many time as needed and replacing the keys by the appropriate exp time

I believe this is what was suggested in this previous thread : Access to arbitrary metadata in Omero

Now I have two questions:

  • Is it the way to go or is there a better option with CellProfiler ?
  • What are these many \x00 \xff\xfe strings found into the cppipe file ? What’s their use ? What do they mean ? It will be a bit annoying when parsing the file



Hi Nicolas

For your last question I bumped into the following post from earlier:


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Dear all,
Many of us have to be tweaking pipelines constantly to optimise for different cell lines or conditions. Wouldn’t it be useful to have a module where to input user defined variables early in the pipeline, or the option to load parameters in a csv and use them as working parameters in modules?

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