Tool for 3d annotations

Hi all,

I am looking for a tool to segment cells (or other structures) in 3d EM images with the following requirements:

  • It should be easy to install and open-source (ideally a Fiji plugin) and decently well documented
  • Simple usage
  • It should support: brush painting, painting outlines and filling them, interpolating shapes in 3d for fast annotations (= propagation of painted shape to next slice(s))

So far, the best fit to these requirements I have found is TrakEM2.
Its only downsides are that it’s quite complicated (because it supports a lot of different features that are not necessary for this task) and that it (as far as I know) does not support interpolation of painted shapes between slices.

I would be very interested to know if anyone has other suggestions for this.
Pinging @Christian_Tischer how might also be interested in this.



Hi Constantin,
try MIB (, which was done exactly for that purpose. Everything you need is there, including Ilastik export and import.