Abstract
Background and objectives: In recent years, electron microscopy is enabling the acquisition of volumetric data with resolving power to directly observe the ultrastructure of intracellular compartments. New insights and knowledge about cell processes that are offered by such data require a comprehensive analysis which is limited by the time-consuming manual segmentation and reconstruction methods.
Method: We present methods for automatic segmentation, reconstruction, and analysis of intracellular compartments from volumetric data obtained by the dual-beam electron microscopy. We specifically address segmentation of fusiform vesicles and the Golgi apparatus, reconstruction of mitochondria and fusiform vesicles, and morphological analysis of the reconstructed mitochondria.
Results and conclusion: Evaluation on the public UroCell dataset demonstrated high accuracy of the proposed methods for segmentation of fusiform vesicles and the Golgi apparatus, as well as for reconstruction of mitochondria and analysis of their shapes, while reconstruction of fusiform vesicles proved to be more challenging. We published an extension of the UroCell dataset with all of the data used in this work, to further contribute to research on automatic analysis of the ultrastructure of intracellular compartments.
Original language | English (US) |
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Pages (from-to) | 106959 |
Journal | Computer Methods and Programs in Biomedicine |
Volume | 223 |
DOIs | |
State | Published - Jun 25 2022 |
Bibliographical note
KAUST Repository Item: Exported on 2022-07-01Acknowledgements: The authors acknowledge the financial support from the Slovenian Research Agency (research core funding no. P3-0108 ) and the support of the NVIDIA Corporation with donation of a Titan V GPU used for this research. We thank Bruno M. Humbel and Caroline Kizilyaprak for their dual-beam expertise. We acknowledge the work of Žiga Lesar, who is the author of the VPT visualization tool that we used to visualize the entire volume.
ASJC Scopus subject areas
- Health Informatics
- Software
- Computer Science Applications