Tracing of neurons - can ilastik do this?

I am looking for a workflow to trace neurons and other cells in EM data. I had the impression that ilastik is more for feature registration and not really suitable to perform tracing, but my boss wants me to look into ilastik. Does someone use ilastik for tracing? Can it even do this?


I think you may have confused elastix with ilastik? The former is good for registration the latter is good for interactive, learning based segmentation.

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Thanks a lot for your reply.
No, I was thinking of ilastik. My terminology probably was not quite correct. I meant segmentation. What I need is a program that can trace cells from section to section. In my impression, people segment all the cells on each section to get a 3D model of the cells.

Hi @Sebastian_Markert,

ilastik works in 3D - so if you supply the data as a 3D image (preferrably in h5 format, that you can export e.g. via our fiji import export plugin). If you’re only interested in a few neurons, then the Carving workflow might be worth looking into. An alternatuve would also be the Multicut. For the latter you need to generate a boundary probability map (e.g. in Pixel Classification). Carving, too can profit from a boundary probability map (as shown here).