This is by design, though in hindsight, for clarity, Filter perhaps should have been called ImageFilter. From the CPA Manual:
The following fields (optional) specify a subset of the images in your experiment from which to fetch and score objects in Classifier. [/quote]
Filter was intended as a way to limit the search space of images (e.g. positive control images or wells) in which to select objects, but not to filter objects themselves.
You probably want to check out the Gate function in Scatterplot. If you REALLY want to, you could also construct a very strict Rule (Edit… -> Rule) that effectively filters out objects, but I don’t recommend this method.
From some old release notes Gates are defined as:
It is discussed here a bit more: