Segmentation of subcellular structures

The goal of the project is to develop visualization and segmentation methods for subcellular structures. The project is a collaboration with Institute of Cell Biology at Faculty of Medicine, University of Ljubljana.

Current research of living cells is focused on their sub-cellular components -- organelles and their functions. A novel focused ion beam microscopy (FIB) technique provides volumetric data with a resolution which is high enough to obtain such information. We want to leverage existing methods from the field of medical image segmentation to aid research of cellular structure with an algorithm for automatic segmentation of cell volumetric FIB data.

YouTube video

References
  • [PDF] M. Ž. Mekuč, C. Bohak, E. Boneš, S. Hudoklin, R. Romih, and M. Marolt, "Automatic segmentation and reconstruction of intracellular compartments in volumetric electron microscopy data," Computer methods and programs in biomedicine, iss. 223, pp. 1-14, 2022.
    [Bibtex] 
    @article{112962819,
author={Manca Žerovnik Mekuč and Ciril Bohak and Eva Boneš and Samo Hudoklin and Rok Romih and Matija Marolt},
year={2022},
pages={1-14},
title={Automatic segmentation and reconstruction of intracellular compartments in volumetric electron microscopy data},
journal={Computer methods and programs in biomedicine},
number={223},
}
  • [PDF] E. Boneš and M. Marolt, "Automatic segmentation of the Golgi apparatus in volumetric data with approximate labels," in TELSIKS 2021 : proceedings of papers : 2021 15th International Conference on Advanced Technologies, Systems and Services in Telecommunications (TELSIKS), Serbia, Niš, October 20 - 22, 2021, 2021, pp. 393-397.
    [Bibtex] 
    @conference{87048451,
author={Eva Boneš and Matija Marolt},
year={2021},
pages={393-397},
title={Automatic segmentation of the Golgi apparatus in volumetric data with approximate labels},
booktitle={TELSIKS 2021 : proceedings of papers : 2021 15th International Conference on Advanced Technologies, Systems and Services in Telecommunications (TELSIKS), Serbia, Niš, October 20 - 22, 2021},
}
  • [PDF] M. Ž. Mekuč, C. Bohak, S. Hudoklin, B. H. Kim, R. Romih, M. Y. Kim, and M. Marolt, "Automatic segmentation of mitochondria and endolysosomes in volumetric electron microscopy data," Computers in Biology and Medicine, iss. 119, pp. 1-11, 2020.
    [Bibtex] 
    @article{1538555331,
author={Manca Žerovnik Mekuč and Ciril Bohak and Samo Hudoklin and Byeong Hak Kim and Rok Romih and Min Young Kim and Matija Marolt},
year={2020},
pages={1-11},
title={Automatic segmentation of mitochondria and endolysosomes in volumetric electron microscopy data},
journal={Computers in Biology and Medicine},
number={119},
}
  • [PDF] M. Ž. Mekuč, C. Bohak, R. Romih, S. Hudoklin, and M. Marolt, "Avtomatska segmentacija celičnih predelkov v volumetričnih podatkih, pridobljenih z elektronskim mikroskopom," Uporabna informatika, vol. 27, iss. 4, pp. 153-156, 2019.
    [Bibtex] 
    @article{1538498243,
author={Manca Žerovnik Mekuč and Ciril Bohak and Rok Romih and Samo Hudoklin and Matija Marolt},
year={2019},
pages={153-156},
volume={27},
title={Avtomatska segmentacija celičnih predelkov v volumetričnih podatkih, pridobljenih z elektronskim mikroskopom},
journal={Uporabna informatika},
number={4},
}
Collaborators

Institute of Cell Biology

test_655