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Fabrice de Chaumont
14 Oct 2013 17:30
Very simple and intuitive. The Youtube example is a good idea to better understand how to use the plugin. Still, the nyan cat background is very ugly :)
26 Apr 2013 10:46

Active Cells 3D

by Biomedical Imaging Group

This plug-in implements fast active surfaces for 3D image segmentation. Their representation in terms of spline surfaces allows for a natural and intiutive manipulation of the surface.

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This software implements a fast active-contour model (a.k.a. snake) for image segmentation in 3D microscopy. The proposed 3D snake can approximate blob-like objects with good accuracy and can perfectly reproduce spheres and ellipsoids, irrespective of their position and orientation. The modification of one control point affects a limited region of the snake surface, which favors intuitive interactions with the user. Since our shape model is fully characterized by few control points, the design of customized shapes becomes possible by simple manipulation of these points in the same way that control points are used in the NURBS meshes typical of computeraided industrial designs.

Written by Ricard Delgado-Gonzalo at the Biomedical Image Group (BIG), EPFL, Switzerland.

Technical Details



R. Delgado-Gonzalo, N. Chenouard, M. Unser, ""Spline-Based Deforming Ellipsoids for Interactive 3D Bioimage Segmentation," IEEE Transactions on Image Processing, vol. 22, no. 10, pp. 3926-3940, October 2013.

R. Delgado-Gonzalo, N. Chenouard, M. Unser, "Fast Parametric Snakes for 3D Microscopy," Proceedings of the Ninth IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'12), Barcelona, Spain, May 2-5, 2012.


This work would not have been possible without the contribution of

  • Nicolas Chenouard (
  • Philippe Thévenaz (
  • Emrah Bostan (
  • Ulugbek S. Kamilov (
  • Ramtin Madani (
  • Masih Nilchian (
  • Cédric Vonesch (
  • Virginie Uhlmann (
  • Michael Unser (