I just joined a research group at MGH. Many of the people here use Cell Profiler but not Matlab and I have been using Matlab for many years. I am trying to help them by automating the pipelines using Matlab. So far they have given me the pipeline (.cp file I think) and I have set up the image folders, input and output etc. I have seen posts about loading pipelines with commands such as:
open('<CellProfiler path>\Cellprofiler.exe -p <Pipeline path>\pipeline_example.cp -c -r -i <images path> -o <output path>')
I get errors when try this and I am assuming it is because I did not install the compiler correctly. There are so many versions of CellProfiler 1.0 and I was wondering if anyone could tell me exactly which one to download and where to save it and how to save and run the compiler. I think I’m just missing something here! I am using Matlab 2010a on a Windows Vista 64 PC and I checked that all image processing toolboxes were installed correctly. Please let me know is there is any other info I can give to help! And thank you so so much!