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Updated: Jun 26, 2026
From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data
Published on: August 13, 2014
A unified framework for automated 3-d segmentation of surface-stained living cells and a comprehensive segmentation
Erlend Hodneland1, Nickolay V Bukoreshtliev, Tilo W Eichler
1Department of Biomedicine, University of Bergen, 5009 Bergen, Norway. erlend.hodneland@biomed.uib.no
Abstract:
This work presents a unified framework for whole cell segmentation of surface stained living cells from 3-D data sets of fluorescent images. Every step of the process is described, image acquisition, prefiltering, ridge enhancement, cell segmentation, and a segmentation evaluation. The segmentation results from two different automated approaches for segmentation are compared to manual segmentation of the same data using a rigorous evaluation scheme. This revealed that combination of the respective cell types with the most suitable microscopy method resulted in high success rates up to 97%. The described approach permits to automatically perform a statistical analysis of various parameters from living cells.
