Unknown

Dataset Information

0

LimeSeg: a coarse-grained lipid membrane simulation for 3D image segmentation.


ABSTRACT: BACKGROUND:3D segmentation is often a prerequisite for 3D object display and quantitative measurements. Yet existing voxel-based methods do not directly give information on the object surface or topology. As for spatially continuous approaches such as level-set, active contours and meshes, although providing surfaces and concise shape description, they are generally not suitable for multiple object segmentation and/or for objects with an irregular shape, which can hamper their adoption by bioimage analysts. RESULTS:We developed LimeSeg, a computationally efficient and spatially continuous 3D segmentation method. LimeSeg is easy-to-use and can process many and/or highly convoluted objects. Based on the concept of SURFace ELements ("Surfels"), 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. The particles are self-generating and self-destructing thus providing the ability for the membrane to evolve towards the contour of the objects of interest. The capabilities of LimeSeg: simultaneous segmentation of numerous non overlapping objects, segmentation of highly convoluted objects and robustness for big datasets are demonstrated on experimental use cases (epithelial cells, brain MRI and FIB-SEM dataset of cellular membrane system respectively). CONCLUSION:In conclusion, we implemented a new and efficient 3D surface reconstruction plugin adapted for various sources of images, which is deployed in the user-friendly and well-known ImageJ environment.

PROVIDER: S-EPMC6318983 | BioStudies |

REPOSITORIES: biostudies

Similar Datasets

| S-EPMC3539759 | BioStudies
| S-EPMC8254216 | BioStudies
| S-EPMC8357924 | BioStudies
| S-EPMC7766091 | BioStudies
| S-EPMC7260992 | BioStudies
| S-EPMC3635992 | BioStudies
| S-EPMC7009784 | BioStudies
2009-01-01 | S-EPMC2647838 | BioStudies
| S-EPMC6190406 | BioStudies
| S-EPMC7203751 | BioStudies