We’re not clear exactly where your problem lies. Let’s first make sure that CPA is working well enough for you.
Once you Find Rules on your training set, and then Fetch Negative and/or Positive objects, does the classifier return decent results? i.e. is the false negative and false positive rate sufficiently low? Basically, you need to be very sure that the classifier works across your whole data set.
[quote]Then I go back to cellprofiler analyst and try to fetch these false-positive cells (to put them in the negative bin) but it does not return them back to me
Note that fetching cells from the negative bin returns a random sampling of objects that the classifier currently assesses as negative. Are you expecting that it will return particular cells? You can choose a particular image (if you know its ImageNumber) and drag particular cells into the negative bin if you like.
Or in CP you can, in Test Mode, choose a particular image set which you know you have classified some cells for and look at CP’s FilterObjects output for that particular image.
** NOTE though**, just because a particular object was placed in, say, the negative bin, once the rules are applied, it is possible that it could be classified as positive, depending on how hard your classification is and how close the cell lies to the classifier’s decision boundary.
In general, please note that CP’s FilterObjects simply uses CPA’s rules as a sort of specialized filter, and that the interplay between the two software packages is almost all from CP -> CPA, except for this singular case where rules can be fed back into FilterObjects.
Does this help?