When using particle counting, is there anyway to save these outlines to a file such that we could manipulate them from MATlab. I notice that CellProfiler does not make use of Workspace, and I am unsure how to access data.


That is a great question. CellProfiler will only save the outlines for the OverlayOutlines module. It does not currently allow you to save the outlines to a file. However, we will look into adding this in the future releases of CellProfiler.

thanks for the suggestion.


although, it does not save these outlines to a file, does it go through the workspace at all. I work frequently in MATLAB, and this is the first time I’ve seen code that doesn’t show up in the workspace. I wondered if you had any suggestions for someone who wants to manipulate it on their own how they might access this data. If I were to try to modify this module myself, do you have any hints as to where in the code I might look to start playing with this.

Thank you,

Eleanor Ory (EChO)


You can find the location stored in handles.Measurements.[NameOfTheObjectYouIdentified].Location. For example, if you identified an object called,“nuclei”, it would be stored in:

For further information on how CellProfiler is organized, please refer to the ‘Developer Information’ section of the CellProfiler manual.