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International Journal of Molecular Sciences, volume 24, issue 2, pages 1102

Deep Semantic Segmentation of Angiogenesis Images

Ibragimov Alisher ¹

Senotrusova Sofya ¹

Markova Kseniia ²

Karpulevich Evgeny ¹

Ivanov Andrei ¹

Tyshchuk Elizaveta ²

Grebenkina P V ²

Stepanova Olga ²

Sirotskaya Anastasia ²

Kovaleva Anastasiia ²

Oshkolova Arina ²

Zementova Maria ²

Konstantinova Viktoriya ²

Kogan I. Yu. ²

Selkov S. A. ²

Sokolov Dmitry I. ²

Hide authors affiliations Show authors affiliations: 2 affiliations

Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences (ISP RAS), 109004 Moscow, Russia |

Department of Immunology and Intercellular Interactions, Federal State Budgetary Scientific Institution, Research Institute of Obstetrics, Gynecology, and Reproductology Named after D.O. Ott, 199034 St. Petersburg, Russia |

Publication type: Journal Article

Publication date: 2023-01-06

Multidisciplinary Digital Publishing Institute (MDPI)

Journal: International Journal of Molecular Sciences

Quartile SCImago

Quartile WOS

Impact factor: 5.6

ISSN: 16616596, 14220067

DOI: 10.3390/ijms24021102

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Catalysis

Organic Chemistry

Inorganic Chemistry

Physical and Theoretical Chemistry

Computer Science Applications

Spectroscopy

Molecular Biology

General Medicine

Abstract

Angiogenesis is the development of new blood vessels from pre-existing ones. It is a complex multifaceted process that is essential for the adequate functioning of human organisms. The investigation of angiogenesis is conducted using various methods. One of the most popular and most serviceable of these methods in vitro is the short-term culture of endothelial cells on Matrigel. However, a significant disadvantage of this method is the manual analysis of a large number of microphotographs. In this regard, it is necessary to develop a technique for automating the annotation of images of capillary-like structures. Despite the increasing use of deep learning in biomedical image analysis, as far as we know, there still has not been a study on the application of this method to angiogenesis images. To the best of our knowledge, this article demonstrates the first tool based on a convolutional Unet++ encoder–decoder architecture for the semantic segmentation of in vitro angiogenesis simulation images followed by the resulting mask postprocessing for data analysis by experts. The first annotated dataset in this field, AngioCells, is also being made publicly available. To create this dataset, participants were recruited into a markup group, an annotation protocol was developed, and an interparticipant agreement study was carried out.

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Ibragimov A. et al. Deep Semantic Segmentation of Angiogenesis Images // International Journal of Molecular Sciences. 2023. Vol. 24. No. 2. p. 1102.

GOST all authors (up to 50) Copy

Ibragimov A., Senotrusova S., Markova K., Karpulevich E., Ivanov A., Tyshchuk E., Grebenkina P. V., Stepanova O., Sirotskaya A., Kovaleva A., Oshkolova A., Zementova M., Konstantinova V., Kogan I. Y., Selkov S. A., Sokolov D. I. Deep Semantic Segmentation of Angiogenesis Images // International Journal of Molecular Sciences. 2023. Vol. 24. No. 2. p. 1102.

RIS |

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RIS Copy

TY - JOUR

DO - 10.3390/ijms24021102

UR - https://doi.org/10.3390%2Fijms24021102

TI - Deep Semantic Segmentation of Angiogenesis Images

T2 - International Journal of Molecular Sciences

AU - Ibragimov, Alisher

AU - Senotrusova, Sofya

AU - Markova, Kseniia

AU - Karpulevich, Evgeny

AU - Ivanov, Andrei

AU - Tyshchuk, Elizaveta

AU - Grebenkina, P V

AU - Stepanova, Olga

AU - Sirotskaya, Anastasia

AU - Kovaleva, Anastasiia

AU - Oshkolova, Arina

AU - Zementova, Maria

AU - Konstantinova, Viktoriya

AU - Kogan, I. Yu.

AU - Selkov, S. A.

AU - Sokolov, Dmitry I.

PY - 2023

DA - 2023/01/06 00:00:00

PB - Multidisciplinary Digital Publishing Institute (MDPI)

SP - 1102

IS - 2

VL - 24

SN - 1661-6596

SN - 1422-0067

ER -

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@article{2023_Ibragimov,

author = {Alisher Ibragimov and Sofya Senotrusova and Kseniia Markova and Evgeny Karpulevich and Andrei Ivanov and Elizaveta Tyshchuk and P V Grebenkina and Olga Stepanova and Anastasia Sirotskaya and Anastasiia Kovaleva and Arina Oshkolova and Maria Zementova and Viktoriya Konstantinova and I. Yu. Kogan and S. A. Selkov and Dmitry I. Sokolov},

title = {Deep Semantic Segmentation of Angiogenesis Images},

journal = {International Journal of Molecular Sciences},

year = {2023},

volume = {24},

publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},

month = {jan},

url = {https://doi.org/10.3390%2Fijms24021102},

number = {2},

pages = {1102},

doi = {10.3390/ijms24021102}

}

MLA

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Ibragimov, Alisher, et al. “Deep Semantic Segmentation of Angiogenesis Images.” International Journal of Molecular Sciences, vol. 24, no. 2, Jan. 2023, p. 1102. https://doi.org/10.3390%2Fijms24021102.

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Publisher

Multidisciplinary Digital Publishing Institute (MDPI)

Journal

International Journal of Molecular Sciences

Quartile SCImago

Quartile WOS

Impact factor

5.6

ISSN

16616596 (Print)
14220067 (Electronic)

Labs

Department of Immunology and Intercellular Interactions

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