Open the handles format pipeline in GUI


Hi team,

We are running CP1. We have some handles files for batch processing and we want to load it into the gui version of CellProfiler. We tried to save only the setting file from the handles but it didn’t load. Can you please guide us how to do it?
We previously saved the handles for running the CP from command line, by doing file–>tech diagnosis and and then run the handles. We now would like to change some parameters in the pipeline, or to add modules and it seems that it will be better to do it through the GUI, the only problem is that we couldn’t open the pipeline that we saved as handles in the gui format in CP.

Thanks for your help,



Hi Maya,
Sorry for the slow response (understatement!), but we haven’t really handled many CP1 queries for the past couple years!
Did you figure this out already? I don’t remember offhand, but you could start CP in Matlab and likely just substitute in your handles structure at a carefully placed debug stop.