LimeSeg is a modular 3D image segmentation method. Based on the idea of SURFace ELements, LimeSeg resembles a highly coarse-grained simulation of a lipid membrane in which a set of particles, analogous to lipid molecules, are attracted to local image maxima.
For the documentation, go to http://imagej.net/LimeSeg/.
LimeSeg is available through Fiji, and is based on a publication. If you use it successfully for your research please be so kind to cite our work (https://doi.org/10.1186/s12859-018-2471-0).