Manca Žerovnik (Author), Ciril Bohak (Author), Eva Boneš (Author), Samo Hudoklin (Author), Rok Romih (Author), Matija Marolt (Author)

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.

Keywords

mikroskopija;mitohondriji;Golgijev aparat;fuziformni vezikli;urotelij;globoko učenje;reconstruction;instance segmentation;electron microscopy;mitochondria;Golgi apparatus;fusiform vesicles;urothelium;deep learning;

Data

Language: English
Year of publishing:
Typology: 1.01 - Original Scientific Article
Organization: UL FRI - Faculty of Computer and Information Science
UDC: 004.8:537.533.35
COBISS: 112962819 Link will open in a new window
ISSN: 0169-2607
Views: 90
Downloads: 46
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Metadata: JSON JSON-RDF JSON-LD TURTLE N-TRIPLES XML RDFA MICRODATA DC-XML DC-RDF RDF

Other data

Secondary language: Slovenian
Secondary keywords: mikroskopija;mitohondriji;Golgijev aparat;fuziformni vezikli;urotelij;globoko učenje;
Type (COBISS): Article
Pages: str. 1-14
Issue: ǂVol. ǂ223
Chronology: Aug. 2022
DOI: 10.1016/j.cmpb.2022.106959
ID: 15776737