The diversity of the objects in my images can be very large (e.g. detection of fruits). That’s why the object detection not always works for all objects. Sometimes I try to overcome this by adding a Flag module to check whether an object is detected or not or it meets some criteria. I can skip the image (if the object is well detected in the first part of the pipeline) or run the last part of the pipeline for objects which are more suited for this type of analysis (the last part of the pipeline after the flag). I have to overwrite the results (mostly an output of saved images) for images which pass the flag criteria.
This is quite an awkward way of running a pipeline. It would be much nicer if it would be possible to run parts of a pipeline based on measured criteria. I mostly use the ClassifyPixels module. It would be nice to use different Classifiers based on some criteria. I know that CellProfiler is not provisioned to work like this but maybe you have any suggestions for me or are there chances that in the future CellProfiler will get such capabilities?