I have generated a classifier in ilastik that works perfectly in ilastik but once exported gives different results during “classify pixels” in cell profiler. I would equate the difference between the two results to the cell profiler result setting a higher “threshold level” than the result that is shown in ilastik (ie. more of the objects are classified as background than are supposed to be). As per previous posts to this board, I have generated the classifier using the ilastik that comes with cell profiler and I am not using any large features (ie. all of my features in ilastik are medium or smaller). Any ideas? It is not like there is a lot to change since all you really are doing up to that point in cell profiler is loading the image and then classifying the pixels. Thanks for any help provided.
Jason T Maynes, PhD/MD
Principal Investigator, Molecular Structure and Function
Hospital for Sick Children