I read the instructions on how to cite CellProfiler and I found in some papers that usually the pipeline the authors used is briefly described in the methods.
I wonder which details should be included concerning the pipeline that was used to obtain the data described in the paper.
In particular, in my case, image analysis will be just a really small section of a part of the paper. The pipeline I used identifies nuclei and cells and calculates mean signal intensity from intracellular staining, after adjusting for background intensity (details here).
Should I just briefly describe what the pipeline does? If yes, should I do so in the methods or in supplementary materials? Is it necessary to include details such as smoothing factor or threshold intensity? If anyone is aware of any paper using CellProfiler for similar purposes, would her/him be so kind as to send me the link, so that I might use it as an example?
Thank you so much for your time!