TEM ExosomeAnalyzer: a computer-assisted software tool for
quantitative evaluation of extracellular vesicles in
transmission electron microscopy images

J 2019

TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images

KOTRBOVÁ, Anna, Karel ŠTĚPKA, Martin MAŠKA, Juraj PÁLENIK, Ladislav ILKOVICS et. al.

Basic information

Original name

TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images

Authors

KOTRBOVÁ, Anna (203 Czech Republic, belonging to the institution), Karel ŠTĚPKA (203 Czech Republic, belonging to the institution), Martin MAŠKA (203 Czech Republic, belonging to the institution), Juraj PÁLENIK (703 Slovakia, belonging to the institution), Ladislav ILKOVICS (203 Czech Republic, belonging to the institution), Dobromila KLEMOVÁ (203 Czech Republic, belonging to the institution), Marek KRAVEC (703 Slovakia, belonging to the institution), František HUBATKA (203 Czech Republic), Zankruti DAVE (356 India, belonging to the institution), Aleš HAMPL (203 Czech Republic, belonging to the institution), Vítězslav BRYJA (203 Czech Republic, belonging to the institution), Pavel MATULA (203 Czech Republic, belonging to the institution) and Vendula POSPÍCHALOVÁ (203 Czech Republic, guarantor, belonging to the institution)

Edition

Journal of Extracellular Vesicles, Taylor and Francis Ltd. 2019, 2001-3078

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10601 Cell biology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Full Text

Impact factor

Impact factor: 14.976

RIV identification code

RIV/00216224:14310/19:00107476

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1080/20013078.2018.1560808

UT WoS

000511377100001

Keywords in English

Exosome; cryo-electron microscopy; extracellular vesicles; image analysis; morphological seeded watershed; negative staining; segmentation; semi-automatic detection; size distribution profile; transmission electron microscopy

Abstract

V originále

Extracellular vesicles (EVs) function as important conveyers of information between cells and thus can be exploited as drug delivery systems or disease biomarkers. Transmission electron microscopy (TEM) remains the gold standard method for visualisation of EVs, however the analysis of individual EVs in TEM images is time-consuming if performed manually. Therefore, we present here a software tool for computer-assisted evaluation of EVs in TEM images. TEM ExosomeAnalyzer detects EVs based on their shape and edge contrast criteria and subsequently analyses their size and roundness. The software tool is compatible with common negative staining protocols and isolation methods used in the field of EV research; even with challenging TEM images (EVs both lighter and darker than the background, images containing artefacts or precipitated stain, etc.). If the fully-automatic analysis fails to produce correct results, users can promptly adjust the detected seeds of EVs as well as their boundaries manually. The performance of our tool was evaluated for three different modes with variable levels of human interaction, using two datasets with various heterogeneity. The semi-automatic mode analyses EVs with high success rate in the homogenous dataset (F1 score 0.9094, Jaccard coefficient 0.8218) as well as in the highly heterogeneous dataset containing EVs isolated from cell culture medium and patient samples (F1 score 0.7619, Jaccard coefficient 0.7553). Moreover, the extracted size distribution profiles of EVs isolated from malignant ascites of ovarian cancer patients overlap with those derived by cryo-EM and are comparable to NTA- and TRPS-derived data. In summary, TEM ExosomeAnalyzer is an easy-to-use software tool for evaluation of many types of vesicular microparticles and is available at http://cbia.fi.muni.cz/exosome-analyzer free of charge for non-commercial and research purposes. The web page contains also detailed description how to use the software tool including a video tutorial.

Links

EF16_013/0001775, research and development project

Name: Modernizace a podpora výzkumných aktivit národní infrastruktury pro biologické a medicínské zobrazování Czech-BioImaging

GJ17-11776Y, research and development project

Name: Funkční a biochemická analýza extracelulárních váčků z ascitů pacientek s karcinomem vaječníku

Investor: Czech Science Foundation

LM2015062, research and development project

Name: Národní infrastruktura pro biologické a medicínské zobrazování

Investor: Ministry of Education, Youth and Sports of the CR

MUNI/E/0876/2018, interní kód MU

Name: TEM ExosomeAnalyzer: Nový software pro kvantitativní charakterizaci extracelulárních vesikulů pomocí transmisní elektronové mikroskopie

Investor: Masaryk University, Promoting quality excellence

MUNI/M/1050/2013, interní kód MU

Name: Automatizovaná analýza elektronmikroskopických snímků pro použití v biologii a medicíně (Acronym: Analýza TEM snímků)

Investor: Masaryk University, INTERDISCIPLINARY - Interdisciplinary research projects

Citovat

KOTRBOVÁ, Anna, Karel ŠTĚPKA, Martin MAŠKA, Juraj PÁLENIK, Ladislav ILKOVICS, Dobromila KLEMOVÁ, Marek KRAVEC, František HUBATKA, Zankruti DAVE, Aleš HAMPL, Vítězslav BRYJA, Pavel MATULA and Vendula POSPÍCHALOVÁ. TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images. Journal of Extracellular Vesicles. Taylor and Francis Ltd., 2019, vol. 8, No 1, p. 1-13. ISSN 2001-3078. Available from: https://dx.doi.org/10.1080/20013078.2018.1560808.

@article{1542776,
   author = {Kotrbová, Anna and Štěpka, Karel and Maška, Martin and Pálenik, Juraj and Ilkovics, Ladislav and Klemová, Dobromila and Kravec, Marek and Hubatka, František and Dave, Zankruti and Hampl, Aleš and Bryja, Vítězslav and Matula, Pavel and Pospíchalová, Vendula},
   article_number = {1},
   doi = {http://dx.doi.org/10.1080/20013078.2018.1560808},
   keywords = {Exosome; cryo-electron microscopy; extracellular vesicles; image analysis; morphological seeded watershed; negative staining; segmentation; semi-automatic detection; size distribution profile; transmission electron microscopy},
   language = {eng},
   issn = {2001-3078},
   journal = {Journal of Extracellular Vesicles},
   title = {TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images},
   url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346710/},
   volume = {8},
   year = {2019}
}

TY  - JOUR
ID  - 1542776
AU  - Kotrbová, Anna - Štěpka, Karel - Maška, Martin - Pálenik, Juraj - Ilkovics, Ladislav - Klemová, Dobromila - Kravec, Marek - Hubatka, František - Dave, Zankruti - Hampl, Aleš - Bryja, Vítězslav - Matula, Pavel - Pospíchalová, Vendula
PY  - 2019
TI  - TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images
JF  - Journal of Extracellular Vesicles
VL  - 8
IS  - 1
SP  - 1-13
EP  - 1-13
PB  - Taylor and Francis Ltd.
SN  - 20013078
KW  - Exosome
KW  - cryo-electron microscopy
KW  - extracellular vesicles
KW  - image analysis
KW  - morphological seeded watershed
KW  - negative staining
KW  - segmentation
KW  - semi-automatic detection
KW  - size distribution profile
KW  - transmission electron microscopy
UR  - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346710/
L2  - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346710/
N2  - Extracellular vesicles (EVs) function as important conveyers of information between cells and thus can be exploited as drug delivery systems or disease biomarkers. Transmission electron microscopy (TEM) remains the gold standard method for visualisation of EVs, however the analysis of individual EVs in TEM images is time-consuming if performed manually. Therefore, we present here a software tool for computer-assisted evaluation of EVs in TEM images. TEM ExosomeAnalyzer detects EVs based on their shape and edge contrast criteria and subsequently analyses their size and roundness. The software tool is compatible with common negative staining protocols and isolation methods used in the field of EV research; even with challenging TEM images (EVs both lighter and darker than the background, images containing artefacts or precipitated stain, etc.). If the fully-automatic analysis fails to produce correct results, users can promptly adjust the detected seeds of EVs as well as their boundaries manually. The performance of our tool was evaluated for three different modes with variable levels of human interaction, using two datasets with various heterogeneity. The semi-automatic mode analyses EVs with high success rate in the homogenous dataset (F1 score 0.9094, Jaccard coefficient 0.8218) as well as in the highly heterogeneous dataset containing EVs isolated from cell culture medium and patient samples (F1 score 0.7619, Jaccard coefficient 0.7553). Moreover, the extracted size distribution profiles of EVs isolated from malignant ascites of ovarian cancer patients overlap with those derived by cryo-EM and are comparable to NTA- and TRPS-derived data. In summary, TEM ExosomeAnalyzer is an easy-to-use software tool for evaluation of many types of vesicular microparticles and is available at http://cbia.fi.muni.cz/exosome-analyzer free of charge for non-commercial and research purposes. The web page contains also detailed description how to use the software tool including a video tutorial.
ER  -

KOTRBOVÁ, Anna, Karel ŠTĚPKA, Martin MAŠKA, Juraj PÁLENIK, Ladislav ILKOVICS, Dobromila KLEMOVÁ, Marek KRAVEC, František HUBATKA, Zankruti DAVE, Aleš HAMPL, Vítězslav BRYJA, Pavel MATULA and Vendula POSPÍCHALOVÁ. TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images. \textit{Journal of Extracellular Vesicles}. Taylor and Francis Ltd., 2019, vol.~8, No~1, p.~1-13. ISSN~2001-3078. Available from: https://dx.doi.org/10.1080/20013078.2018.1560808.

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