CellProfiler 2.1 Pipeline and CSV export

From my first trials, CP 2.1 seems to be a nice piece of software, good job. However, there are two small things that are bugging me:

1. Pipeline export / git version control

I’m using git to version control my pipelines, which has worked pretty well so far. In CP 2.1, everything is organized in projects with individual entries, making it hard to version control it properly. I can export to pipelines, but first it doesn’t have a keyboard shortcut and second, the field (I’m on Mac) does not remember the file name, it always says “pipeline.cppipe”. It would be great to have an (easy) keyboard shortcut to save (not “Save as …”) the pipeline, and not the project, with one keystroke.

One little detail from the previous CP version: The module description has a position indicator in it:

So every time I remove or insert a module, all other module headers get changed, thus appearing in the commit, which is imho not necessary. Is the module_num field really necessary, or is CP able to find the module order by “order of appearance” in the pipeline file?

2. CSV export

The new version of the CSV export has two header rows. While this is clearly easier to overlook, it makes extra steps necessary to import these files in programs such as R. R can only handle one header row. It would be awesome to have a setting in the next version that can revert back to the way it was in the previous CP version.

Thanks a lot and keep up the good work. I want to let you know that CP saved my PhD thesis.


Hi Till,

Glad CP has helped you! Your export pipeline requests seem reasonable and I have added them to our Github issues: github.com/CellProfiler/CellPro … ssues/1042
We’ll try to update this thread if/when we update this. and then you could download an updated “trunk” version.

The module_num is pretty baked-in the code at this point, and yes I’m pretty sure CP cannot just read the order of the pipeline from the order in the .cppipe file. You could try stripping it from the file and it may import properly, but once you export it again it will have the module_num field. I understand that makes the svn commit bigger than it might be at it’s most efficient, but efficient svn commits are not a standard user request :smile: and combined with the large code integration of module_num, it is unlikely to change.

As for the “CSV export”, I just tested both ExportToSpreadsheet and File->Export->Image Set Listing… and in both cases there was only a single header line in the output. Can you elaborate on what CSV export you are referring to?


Oh, and for a workaround for the Keyboard Shortcut, you might try this hack:
Not sure if it will work for this menu item though.

The keyboard shortcut has been added to CP. You can try it in a recent trunk build here: github.com/CellProfiler/CellPro … TrunkBuild

Additionally the pipeline/project naming scheme has been updated accordingly to synchronize between the project and pipeline:


This issue has been resolved with the 2.1.1 release.