Deconvolving snakes in MATLAB

MATLAB code for deconvolving snakes

We provide here the original MATLAB implementation of deconvolving snakes as developed and written by Jo Helmuth as part of his PhD project at the MOSAIC Group:

J. A. Helmuth. Computational Methods for Analyzing and Simulating Intra-Cellular Transport Processes. PhD thesis, Diss. ETH No. 19190, ETH Zürich, 2010. (PDF)


The method is described in the following publications:

J. A. Helmuth, C. J. Burckhardt, U. F. Greber, and I. F. Sbalzarini. Shape reconstruction of subcellular structures from live cell fluorescence microscopy images. Journal of Structural Biology, 167:1–10, 2009. (PDF)

J. A. Helmuth and I. F. Sbalzarini. Deconvolving active contours for fluorescence microscopy images. In Proc. Intl. Symp. Visual Computing (ISVC), volume 5875 of Lecture Notes in Computer Science, pages 544–553, Las Vegas, USA, November 2009. Springer. (PDF)


The MATLAB code provided here is the one that was used for the above publications. It is provided here for completeness and reproducibility. Please notice, however, that the method has meanwhile evolved and is now also available in 3D, and in formulations that do not require the initial segmentation to be topologically correct. The MOSAIC Suite for ImageJ and Fiji contains both the region-competition and the split-Bregman implementation of deconvolving segmentation in 2D and 3D. The Region-competition version works for multiple regions. The split-Bregman version is available for the two-region case, but it is globally convex and hence completely independent of initialization. A fast C++ implementation of the region-competition code is also available as an ITK filter.


In order to ensure financial support for our project and allow further development of this software, please cite above publications in all your documents and manuscripts that made use of this software. Thanks a lot!


IN NO EVENT SHALL THE MOSAIC GROUP BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE MOSAIC GROUP HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. THE MOSAIC GROUP SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE MOSAIC GROUP HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.