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.Základní údaje
Originální název
TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images
Autoři
KOTRBOVÁ, Anna (203 Česká republika, domácí), Karel ŠTĚPKA (203 Česká republika, domácí), Martin MAŠKA (203 Česká republika, domácí), Juraj PÁLENIK (703 Slovensko, domácí), Ladislav ILKOVICS (203 Česká republika, domácí), Dobromila KLEMOVÁ (203 Česká republika, domácí), Marek KRAVEC (703 Slovensko, domácí), František HUBATKA (203 Česká republika), Zankruti DAVE (356 Indie, domácí), Aleš HAMPL (203 Česká republika, domácí), Vítězslav BRYJA (203 Česká republika, domácí), Pavel MATULA (203 Česká republika, domácí) a Vendula POSPÍCHALOVÁ (203 Česká republika, garant, domácí)
Vydání
Journal of Extracellular Vesicles, Taylor and Francis Ltd. 2019, 2001-3078
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10601 Cell biology
Stát vydavatele
Velká Británie a Severní Irsko
Utajení
není předmětem státního či obchodního tajemství
Odkazy
Impakt faktor
Impact factor: 14.976
Kód RIV
RIV/00216224:14310/19:00107476
Organizační jednotka
Přírodovědecká fakulta
UT WoS
000511377100001
Klíčová slova anglicky
Exosome; cryo-electron microscopy; extracellular vesicles; image analysis; morphological seeded watershed; negative staining; segmentation; semi-automatic detection; size distribution profile; transmission electron microscopy
Příznaky
Mezinárodní význam, Recenzováno
Změněno: 9. 2. 2022 09:11, doc. RNDr. Pavel Matula, Ph.D.
Anotace
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.
Návaznosti
| EF16_013/0001775, projekt VaV |
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| GJ17-11776Y, projekt VaV |
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| LM2015062, projekt VaV |
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| MUNI/E/0876/2018, interní kód MU |
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| MUNI/M/1050/2013, interní kód MU |
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