Completely new to Cell profiler: I need to use a pipeline but it is in a word document; when I import it the modules don’t appear in the pipeline panel. I tried converting the file to csv format but this didn’t help. Any ideas?
CellProfiler pipelines are saved in a plain text file with a specific structure and .cppipe extension. Assuming your Word document has preserved the internal text structure, you could try exporting it from Word as a plain text file with a .cppipe extension.
Thanks for your reply, I tried that just now with the same result. I’ve linked the pipeline I’m attempting to use: http://journals.plos.org/plosone/article/file?type=supplementary&id=info:doi/10.1371/journal.pone.0028694.s010
This doesn’t look like a CellProfiler pipeline file but seems to be a list of steps/instructions to follow to reproduce the analysis. You’ll have to follow these manually.
It also appears to have been a set of instructions for CellProfiler1.0, for which some of the modules have slightly different names- Identify Prim Automatic is now IdentifyPrimaryObjects, for example. The names haven’t changed MUCH, so it should be relatively intuitive, if not you can use the help search.
Thanks, I’m not very confident about recreating these steps but I’ll give it a go.
Thanks, I guess if I can’t find a certain module it shouldn’t be hard to find the new name