Loading a pipeline


Hi, I am a new user of cellProfiler.

I made a new pipeline and saved it in a folder, and then later when I tried to re-open the pipe line by using loading pipeline menu, it was giving a error message saying “The file D:\research\pipe.mat is not a valid setting or output file. Settings can be extracted from an output file created when analyzing images with CellProfiler or from a small setting file saved using the “Save Settings” button”.

What does this message mean and what is the problem?


Hi Jay,

There are a couple possibilities. The most obvious is that it really isn’t a pipeline file, maybe you are trying to open a preferences file? If you are certain you saved the pipeline (should end in PIPE.mat), then it is possible that CellProfiler made a mistake. Sometimes when you add and remove several modules, mistakes can occur. We remove bugs as soon as we find them and this happens very rarely now, but it is definitely possible. Try saving another simple pipeline and opening it. If that works, try to re-create your previous pipeline and save it again. If that fails to load, then let us know the exact steps you took to create the problem and we will fix it.

Sorry I couldn’t be more help!



Thanks for the advice.

The thing is that the failure does not always occur and i am not sure what steps are causing the failure. I have been trying to reproduce the failure, but it does not always happen, however it seems like when I make changes in the modules and save the pipeline, sometimes it fails to re-open.

I guess for now it is wise to make backups when I make changes so that I don’t loose the settings all at once.



Yes, it would be wise to backup important pipelines. But please report here if you can reproduce these errors, as we will be able to fix them!