Segmentation of electron microscopy data

segemntation-microscopy

Partner: Institute of Cell Biology
Date: Ongoing

In our work on segmentation of electron microscopy data, we have developed advanced algorithms for both semantic and instance segmentation of four cellular structures - fusiform vesicles, mitochondria, endolysosomes, and the Golgi apparatus. These algorithms, developed for segmentation of volumetric focused ion beam scanning electron microscopy (FIB-SEM) data of urothelial cells, allow for precise identification and characterization of these compartments. Additionally, we have developed specialized algorithms for the shape analysis of mitochondria, providing further insights into cellular structure and function.

One of the key contributions of this project is Urocell, an open-source dataset available at Urocell GitHub. This resource supports segmentation tasks and fosters collaboration across the research community.

Current Research Initiatives

Expanding Segmentation Methods: Broaden segmentation techniques to cover additional cellular compartments, such as membranes, to support more comprehensive cellular analyses.
Refining Instance Segmentation Algorithms: Enhance segmentation algorithms to improve accuracy and efficiency, facilitating more reliable analysis of cellular structures.
Develop a Comprehensive Analysis Pipeline: Build an integrated analysis pipeline tailored to cellular biologists' workflows, enabling high-throughput, reproducible studies.
Collaborating with the Institute for Biology, University of Ljubljana: Partner with experts to explore advanced segmentation techniques for a diverse range of cellular structures, contributing to cutting-edge biological research.

This project represents a significant advancement in computational tools for cellular biology, offering invaluable resources and innovations to the life sciences community.

If you're interested in contributing to this exciting research—whether as part of your diploma or master's thesis or simply as a hobby—please reach out to us! We would love to discuss how you could get involved. Contact Ciril or Manca.

Bibliography

Mekuč, M. Ž., Bohak, C., Boneš, E., Hudoklin, S., Romih, R., & Marolt, M. (2022). Automatic segmentation and reconstruction of intracellular compartments in volumetric electron microscopy data. Computer Methods and Programs in Biomedicine, (223), 1–14. https://doi.org/10.1016/j.cmpb.2022.106959

BibTex

@article{112962819,
	author = {Meku{\v c}, Manca {\v Z}erovnik and Bohak, Ciril and Bone{\v s}, Eva and Hudoklin, Samo and Romih, Rok and Marolt, Matija},
	journal = {Computer methods and programs in biomedicine},
	doi = {10.1016/j.cmpb.2022.106959},
	number = {223},
	year = {2022},
	pages = {1--14},
	title = {Automatic segmentation and reconstruction of intracellular compartments in volumetric electron microscopy data},
}

Boneš, E., & Marolt, M. (2021). Automatic segmentation of the Golgi apparatus in volumetric data with approximate labels. TELSIKS 2021 : Proceedings of Papers : 2021 15th International Conference on Advanced Technologies, Systems and Services in Telecommunications (TELSIKS), Serbia, Niš, October 20 - 22, 2021, 393–397. https://doi.org/10.1109/TELSIKS52058.2021.9606279

BibTex

@inproceedings{87048451,
	author = {Bone{\v s}, Eva and Marolt, Matija},
	booktitle = {TELSIKS 2021 : proceedings of papers : 2021 15th {International} {Conference} on {Advanced} {Technologies}, {Systems} and {Services} in {Telecommunications} ({TELSIKS}), {Serbia}, {Ni}{\v s}, {October} 20 - 22, 2021},
	doi = {10.1109/TELSIKS52058.2021.9606279},
	year = {2021},
	pages = {393--397},
	title = {Automatic segmentation of the {Golgi} apparatus in volumetric data with approximate labels},
}

Mekuč, M. Ž., Bohak, C., Hudoklin, S., Kim, B. H., Romih, R., Kim, M. Y., & Marolt, M. (2020). Automatic segmentation of mitochondria and endolysosomes in volumetric electron microscopy data. Computers in Biology and Medicine, (119), 1–11. https://doi.org/10.1016/j.compbiomed.2020.103693

BibTex

@article{1538555331,
	author = {Meku{\v c}, Manca {\v Z}erovnik and Bohak, Ciril and Hudoklin, Samo and Kim, Byeong Hak and Romih, Rok and Kim, Min Young and Marolt, Matija},
	journal = {Computers in biology and medicine},
	doi = {10.1016/j.compbiomed.2020.103693},
	number = {119},
	year = {2020},
	pages = {1--11},
	title = {Automatic segmentation of mitochondria and endolysosomes in volumetric electron microscopy data},
}

Boneš, E. (2020). Avtomatska segmentacija Golgijevih aparatov v volumetričnih podatkih z grobo označenim zlatim standardom. Zbornik Devetindvajsete Mednarodne Elektrotehniške in Računalniške Konference ERK 2020 = Proceedings of the Twenty-Ninth International Electrotechnical and Computer Science Conference ERK 2020, 448–451.

BibTex

@inproceedings{29391363,
	author = {Bone{\v s}, Eva},
	booktitle = {Zbornik devetindvajsete mednarodne {Elektrotehni}{\v s}ke in ra{\v c}unalni{\v s}ke konference {ERK} 2020 = {Proceedings} of the {Twenty}-ninth {International} {Electrotechnical} and {Computer} {Science} {Conference} {ERK} 2020},
	year = {2020},
	pages = {448--451},
	title = {Avtomatska segmentacija {Golgijevih} aparatov v volumetri{\v c}nih podatkih z grobo ozna{\v c}enim zlatim standardom},
}

Mekuč, M. Ž., Bohak, C., Romih, R., Hudoklin, S., & Marolt, M. (2019). Avtomatska segmentacija celičnih predelkov v volumetričnih podatkih, pridobljenih z elektronskim mikroskopom. Uporabna Informatika, 27(4), 153–156.

BibTex

@article{1538498243,
	author = {Meku{\v c}, Manca {\v Z}erovnik and Bohak, Ciril and Romih, Rok and Hudoklin, Samo and Marolt, Matija},
	journal = {Uporabna informatika},
	number = {4},
	year = {2019},
	pages = {153--156},
	title = {Avtomatska segmentacija celi{\v c}nih predelkov v volumetri{\v c}nih podatkih, pridobljenih z elektronskim mikroskopom},
	volume = {27},
}