Add a `How to adapt workflow to new data` section about imcsegmentationpipeline

[paulamartingonzalez]

Dear Votti, I have been trying to run the pipeline on my own IMC images (I have them already in tiff version) and I am receiving the following error in CellProfiler preprocessing pipeline:

"The pipeline cannot be started because of a configuration problem:The pipeline did not identify any image sets. Please correct any problems in your input module settings and try again."

I added the files to the file list already. It is working in your test data. Do you have any suggestions of what is missing? Thx in advance

[votti]

Hi!
How did you convert them to .tiff?
The Cellprofiler pipelines rely on the standardized naming that comes out from preprocessing the tiff files using these scripts.
If you use a custom naming, you need to adapt the way cellprofiler identifies images, namely the Metadata section and/or the NamesAndTypes section.

CellProfiler preprocessing pipeline: which step do you mean? 1_prepare_ilastik? There one would need to change how image stacks to be used for ilastik are identified. -> Change the Select the rule criteria section.