Select cells from features and save only selected features


Here is a very important question:

Let’s suppose I want to filter and select cells that have certain brightness in two different channels. These two features are not one within another. I want to get the cells that are containing these 2 features and collect all the possible statistics about the shape of the 2 features inside each cell and the “relate” indicating which one is the cell that “owns” these features. I read the documentation and I could not find a perfect way of doing that.

I already have objects for Feature_1 and for Feature_2. I also have the objects that are Cells. Now, I want to filter and only save Cells that contain Feature_1 and Feature_2 inside and collect the statistics of this feature shapes (but only the ones that belong to cells with both of them). Finally, I will “relate” them in order to know which cell corresponds to which features.

Thank you for your help.



Hi Joaquin,

This relates to the question you asked about filtering objects that only have another object present. Again, I think this is something that is easily addressed in post-processing of your data. If you really want to have CellProfiler throw away these objects, I would probably filter your Cells by max intensity in both Feature_1 and Feature_2 images. So you would have original Cells, then filter by Feature_1 max intensity and have Cells_1, then filter Cells_1 by Feature_2 max intensity.

Hope this helps,