Cell segmentation : Ilastik vs Weka vs Orbit


I am working on lymphocytes’ phenotype on tissu slides and my major concern is to obtain a good segmentation of these cells.

I have tested weka and ilastik with pretty good results but it take a lot of time to work with two soft in parallel and I have to choose now!

In your opino, whitch one will be the more performant and stable after full training?

And what’s about « Orbit »



Hi Philippe,

ilastik I found it quite fast but you mostly need to convert to hdf5 in order to analyse the images. Weka works nice and you are in the imageJ/Knime world. So you can perform a lot more of post-processing steps. Orbit I don’t know.
About output performance I was not able to see a big difference but it depends on which filters are used for the training. Best is to try it out with the same training set. At the end I often use Weka if I want to a have a complete pipeline in one software.